Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate GFF440 HP15_428 glutamine synthetase, type I
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__Marino:GFF440 Length = 467 Score = 130 bits (326), Expect = 1e-34 Identities = 120/403 (29%), Positives = 170/403 (42%), Gaps = 52/403 (12%) Query: 66 GVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTP-VAISPRRVLRRVLELYKAK 124 G+ + DM+ +PD T + P+ + T + + V PR V RR E K+ Sbjct: 58 GINESDMILMPDDETSVLDPFTEETTVNITCNIVEPSTMQGYERDPRSVARRAEEYLKST 117 Query: 125 GWKP--VIAPELEFYLVDM---NKDPDLPL-----------------QPPIGRTGRPETG 162 G + PE EF++ D N D + + IG RP Sbjct: 118 GIADGALFGPEPEFFVFDSVKWNVDMQGAMYHIHSEEAAWVSGEDFDRNNIGH--RPGVK 175 Query: 163 RQAYSIEAVNEFDPLFEDIYEYCEVQELEVDTLIHEVGAA-QMEINFMHGDPLKLADSVF 221 + + V+ L + E L+++ HEVG A Q EI K AD V Sbjct: 176 GGYFPVPPVDSLHDLRGAMCAAMESMGLDIEVHHHEVGTAGQCEIGVGANTLTKKADEVQ 235 Query: 222 LFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKPTS-LF 280 + K V A + ATFM KP+ G+ GS MH+H SL + G NLF G S Sbjct: 236 ILKYCVHNVAHAYGKTATFMPKPVVGDNGSGMHVHMSL--SKDGKNLFAGDSYAGLSEAA 293 Query: 281 TSYIAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPH-SGPAAR 339 YI G+ K+ A+ NSY+RL AP+ +A+ NR+ RIP+ + P AR Sbjct: 294 LYYIGGVIKHAKAINAFTNSSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPKAR 353 Query: 340 RIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPLLSDGYELPYQLPRNLEEGLTLM 399 RIE R P NPYLA AA + AG G+ K+ + + D Y+LP EE L++ Sbjct: 354 RIEVRFPDPSANPYLAFAALMMAGLDGIQNKIHPGDAMDKDLYDLP------KEEALSIP 407 Query: 400 GACEPIAEVLG----------------EKFVKAYLALKETEYE 426 E ++E L E + Y+ LK E E Sbjct: 408 TVAETLSEALDCLEADHEFLTRGGVFTEDMIAGYVGLKRGEVE 450 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: 512 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 444 Length of database: 467 Length adjustment: 33 Effective length of query: 411 Effective length of database: 434 Effective search space: 178374 Effective search space used: 178374 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