Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate 6939323 Sama_3416 glutamine synthetase (RefSeq)
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__SB2B:6939323 Length = 469 Score = 136 bits (343), Expect = 1e-36 Identities = 130/426 (30%), Positives = 182/426 (42%), Gaps = 49/426 (11%) Query: 47 QAVMIQT--VTGDYPEDGTL---------TGVTDPDMVCVPDASTIRMIPWAVDPTAQVI 95 Q V I T V D+ EDG + G+ + DMV +PDA+T + P+ + TA + Sbjct: 30 QHVSIPTHQVDADFFEDGKMFDGSSIAGWKGINESDMVLMPDATTFVLDPFTEETTAIIR 89 Query: 96 HDCVHFDGTPVAIS--PRRVLRRVLELYKAKGWKPVI--APELEFYLVD-MNKDPDLP-- 148 D + GT PR + ++ E +A G + PE EF+L D + D+ Sbjct: 90 CDILE-PGTMTGYDRDPRSIAKKAEEYLRATGIADTVLMGPEPEFFLFDDVRFGTDMSGT 148 Query: 149 --------------LQPPIGRTG-RPETGRQAYSIEAVNEFDPLFEDIYEYCEVQELEVD 193 G TG RP + + V+ L + E V+ Sbjct: 149 FVKIDAKEAAWNSSTSYEDGNTGHRPFVKGGYFPVAPVDSSQDLRSAMCLVLEEMGQVVE 208 Query: 194 TLIHEVGAA-QMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPMEGEPGSA 252 HEV A Q EI K AD + + K V A + ATFM KP+ G+ GS Sbjct: 209 AHHHEVATAGQNEIATRFNTLTKKADEIQILKYVVHNMAHAYGKTATFMPKPIVGDNGSG 268 Query: 253 MHMHQSLVDEETGHNLFTGPD-GKPTSLFTSYIAGLQKYTPALMPIFAPYINSYRRLSRF 311 MH+HQSL + G NLF G G + YI G+ K+ AL P NSY+RL Sbjct: 269 MHVHQSLAKD--GVNLFAGDKYGGLSETALYYIGGIIKHARALNAFTNPSTNSYKRLVPH 326 Query: 312 MAAPINVAWGYDNRTVGFRIP-HSGPAARRIENRIPGVDCNPYLAIAATLAAGYLGMTQK 370 AP+ +A+ NR+ RIP P RRIE R P NPYL AA L AG G+ K Sbjct: 327 FEAPVMLAYSARNRSASIRIPVVPSPKGRRIETRFPDPTANPYLGFAALLMAGLDGIQNK 386 Query: 371 LEATEPLLSDGYELPYQ-------LPRNLEEGLTLMGACEPI---AEVLGEKFVKAYLAL 420 + + + D Y+LP + + +L+ L + A V F+ +Y+ L Sbjct: 387 IHPGDAMDKDLYDLPAEEAAEIPTVAESLDVALAALDADREFLTKGGVFSNDFIDSYIRL 446 Query: 421 KETEYE 426 K E E Sbjct: 447 KTAEAE 452 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: 505 Number of extensions: 29 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: 469 Length adjustment: 33 Effective length of query: 411 Effective length of database: 436 Effective search space: 179196 Effective search space used: 179196 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