GLY1-6a0befc5 (GLY1)

The raw output files for each step of the pipeline can be found here.

Input: sequence:

>GLY 1-830 Saccharomyces cerevisiae S288C
TTACAATTACGGATGAGGGGTTGTTGAAGTGAAGATAAGAAAAAAAAATGGGGTGCTATG
TCAGCGTATTGTTCTCAGCTTTTATACGTGCAATAGATTAAGCTGTTCAGGAACGCGACG
CGTTGCCCCCGTTACCGTTTGAAAAGAAAAAAATTTTCTTTTTCATACCTGTCTCTATTG
TTTCAGTCATTCACTGCATGATGACAAATGAAAGAAGAAAGACAATAGTAGTAAAAGCAA
AAAAGGAATTAAAGTGAACGTTTTTTAGACTCTTACGCATACATATAAATATATATATAT
ATTTGTATAAAAGGTGTACGTCGAAATCCTGTGAAGAAACCCTGCGAGAATATACATGGG
TACATTCAATCTTAATACGTAGTATCGTAGAATACAAAGAAATGTGCTTCTCCACGTGGA
TACGTACCGTTGTAAACTTTAATCAAGTACCAAAAAAACCAAACATATTCAGTCGATCTC
TCAATGGGGAACAAAGAAAAGAGGTTCTTACCTTTTTTTCCTCCTTCCCTCAGAAAGACC
ACCTTCGTCCCTCCATAATAGGGTAGTTAGTCGCTAGGTGCGCTGGAAACTAACCATTGG
TTCTCAAATGTGCCGACATAATTAGTTATAATTATGGTGTGAGAGTTGAAATATCCTTGA
ATAACAAAACAGAAAAAAGAAAAAACCCATTTGAATATAAAAATCATTGATGCAAAAGAA
AGCCGTTAAATCTACAATGCCACGAAATTATTGTAATGTATGAAAAAAAGGAAGAGGGTA
GCAATCCTAAAACAAAAACCCTAACAATACACATGATGCAACTGGAACGCATCAGTATTT
GTAGGTTTTTATTTCGCGGATAGCGTTGCCATCAACGTCGACCTCGGTGGATTCACTACG
GTAAATCTGGGTAGGTCCGTTACAGTCGAAAGGATGTTCTTTAGCATAGTCGAAGGCCTC
GGAGATGGCCAATTTGACTTTTTCCAAAGTATCTCTGGTGACTTGATAGTGGAACGAGAC
TCTACCACCCATTAGCTTAACGTTGTACTTCAAACCCTTCTTAACAAGGACATCTGGGTC
CATTCTAGCGGCCTTCAGGTTAATAAAGACAAAGTTGGTGTCTGCTGGAGACTCTAGCGG
GATGCCCTTTGCCTCACAATATTCGGCTAATTCATGAGCCAAAGAGTGCGAGTACAGCAA
TTGGGACTTCCAATCGTTGTTGATGTTTACAAGAGCCATTCTAGCCATCATACCAGATTG
TCTAATACCACCACCTTGTTGTTTTCTGAAATGGGTGGCCTTCTTGACAAACTTAAGGTT
CCCAACCAAGACGGACCCAATAGGAGCACCCATAGACTTGGATAGACAGATGGAGATGGA
GTCGAAGATTTCCCCATATTGCTTTAATGGCACGCCAGATTGTGCAGCGGCATTCCAGAT
TCTGGCACCGTCACAATGTAGTTTGAGACCATTTTCCATACACCAAGCTTTGATGCGGAC
CAGTTCTTCCAATGGATAAACAATACCGTGTAAAGTGTTTTCCAGAGAAATCAATCTGGT
GGGGGCACCGTGAATATCACCGTCGTCTGGGACGTAGTGTGACTTGATGTCTTCCAAGGT
CAAGTAGTCACCGTTGGAAGGAACCACAGGAACCACCATCGCTTGAGACAAGATCGCCAG
TCCAGCGGCTTCGTGAGTGTAAACGTGAGCCCTGTAATCACATAGAATAGAGTATGGAGG
TTGCATCAAGTGAGTTCTGATGGCAATCTGGTTGGACAAAGTCCCAGAGACACAGAACAA
ACCTGCTTCTTTGCCAGCCATGCGGGCAACGGTCTGTTCGAGCCTAACGGTGTCAACATC
TTCACCGTAGACAGCGTCACCGATAGAGGCCTCTAAAGCGGCCTCCATCATCTCTGCAGT
TGGAGTGGTGAATGTGTCTGACCGCAAGTCGTTAGCAGCGGTGATATATTTTGGAGGCAA
TTCGAATTCAGTCA

Database: yeast

---

PDB hits:

No hits were detected to the PDB database!

Rfam hits:

No hits were detected to the Rfam database!

R-scape on nhmmer alignment:

The final nhmmer alignment can be found here.

Alignments from each iteration: iteration 1, iteration 2, iteration 3.

List of covarying basepairs (#6)

In given structure	Left Position	Right Position	Score	E-value	p-value	Substitutions	Power
~	780	1248	58.29493	3.01808e-06	2.72673e-11	4	0.07
~	782	1246	41.81051	0.00512296	4.62841e-08	8	0.24
~	799	1027	61.28606	7.74588e-07	6.99813e-12	25	0.67
~	800	1026	81.86878	6.70104e-11	6.05415e-16	30	0.74
~	801	1025	41.45384	0.00599775	5.41876e-08	43	0.83
~	1065	1244	39.84786	0.0126051	1.13883e-07	3	0.02

* Base pair in the structure
~ Both residues unpaired in the structure, or no structure is present
' ' At least one residue is involved in other pairing in the structure

BPAIRS 80
avg substitutions per BP  18.1
BPAIRS expected to covary 38.7 +/- 3.9
BPAIRS observed to covary 6

Alignment statistics:

Alignment number:    1
Alignment name:      GLY
Format:              Stockholm
Number of sequences: 66
Alignment length:    2188
Total # residues:    26511
Smallest:            167
Largest:             839
Average length:      401.7
Average identity:    43%

R-scape on infernal alignment:

The Infernal alignment can be found here.

List of covarying basepairs (#7)

In given structure	Left Position	Right Position	Score	E-value	p-value	Substitutions	Power
*	494	834	61.31803	2.31063e-07	1.73901e-12	6	0.16
*	496	832	40.80186	0.00425865	3.20513e-08	8	0.24
*	513	630	63.48968	8.22542e-08	6.19058e-13	24	0.66
*	514	629	82.38670	9.26564e-12	6.97346e-17	26	0.69
*	515	628	38.18115	0.0150677	1.13402e-07	43	0.83
*	516	627	43.53980	0.00117284	8.82696e-09	49	0.86
*	661	828	36.81608	0.0286548	2.15661e-07	17	0.52

* Base pair in the structure
~ Both residues unpaired in the structure, or no structure is present
' ' At least one residue is involved in other pairing in the structure

BPAIRS 56
avg substitutions per BP  17.9
BPAIRS expected to covary 26.3 +/- 3.2
BPAIRS observed to covary 7

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