Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate BPHYT_RS12945 BPHYT_RS12945 glutamine synthetase
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__BFirm:BPHYT_RS12945 Length = 471 Score = 134 bits (337), Expect = 6e-36 Identities = 134/465 (28%), Positives = 195/465 (41%), Gaps = 54/465 (11%) Query: 3 DIDDFLKKNRVTEIEAIIPDMAGIARGKIIPRS-----KFESGESMRLPQAVMIQTVTGD 57 D+ +K V ++ D G + +P S KFESG + D Sbjct: 7 DVVQLVKDEDVKFVDFRFTDTRGKEQHVSVPVSAFDEDKFESGHAF-------------D 53 Query: 58 YPEDGTLTGVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVH-FDGTPVAISPRRVLRR 116 G+ DM+ VPDA+T + P+ + T + D V DG PR + +R Sbjct: 54 GSSIAGWKGIEASDMLLVPDANTAFIDPFYEESTLVLTCDVVEPADGKGYERDPRSLAKR 113 Query: 117 VLELYKAKGWKPV--IAPELEFYLVDM---NKDP----------DLPLQPPI----GRTG 157 K+ G PE EF++ D N D + P G TG Sbjct: 114 AEAYLKSTGLGDTAFFGPEPEFFIFDSVQWNTDQSGCFIKIGSEEAPWSSAKEFEGGNTG 173 Query: 158 -RPETGRQAYSIEAVNEFDPLFEDIYEYCEVQELEVDTLIHEV-GAAQMEINFMHGDPLK 215 RP T + + V+ F + ++ E + V+ HEV G Q EI ++ Sbjct: 174 HRPGTKGGYFPVAPVDTFQDIRSEMCLLLEQIGIPVEVHHHEVAGQGQNEIGTKFSTLVQ 233 Query: 216 LADSVFLFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGK 275 AD + K + A + ATFM KP+ G+ GS MH+HQS+ + G NLF G Sbjct: 234 RADWLQQMKYIIHNVAHTYGKTATFMPKPVVGDNGSGMHVHQSIWKD--GANLFAGNGYA 291 Query: 276 PTSLFTS-YIAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPH- 333 S F YI G+ K+ AL I P NSY+RL AP+ +A+ NR+ RIPH Sbjct: 292 GLSEFALFYIGGIIKHARALNAITNPSTNSYKRLVPHFEAPVKLAYSARNRSASIRIPHV 351 Query: 334 SGPAARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPLLSDGYELPYQ------ 387 S P RRIE R P NPYL +A + AG G+ K+ E + Y+LP + Sbjct: 352 SNPKGRRIETRFPDPMANPYLCFSALMMAGLDGVQNKIHPGEAADKNLYDLPPEEDAKIP 411 Query: 388 -LPRNLEEGLTLMGACEPI---AEVLGEKFVKAYLALKETEYEAF 428 + L++ L + A V + + AY+ LK E + + Sbjct: 412 TVCAGLDQALDALDADREFLTRGGVFTDSMLDAYIELKTGELQRY 456 Lambda K H 0.321 0.138 0.418 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 529 Number of extensions: 32 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 444 Length of database: 471 Length adjustment: 33 Effective length of query: 411 Effective length of database: 438 Effective search space: 180018 Effective search space used: 180018 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory