Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate WP_025763368.1 X939_RS0111240 glutamine synthetase
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >NCBI__GCF_000566685.1:WP_025763368.1 Length = 453 Score = 185 bits (469), Expect = 3e-51 Identities = 129/379 (34%), Positives = 190/379 (50%), Gaps = 21/379 (5%) Query: 71 DMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAI-SPRRVLRRVLELYKAKGWKPV 129 D VPD ST+R+ W +D TA V+ D V + I +PR +L++ LE Sbjct: 79 DFHMVPDLSTLRIADW-LDKTAMVLCDLVDEKNHSLDIVAPRSILKKQLEAVAQDELACF 137 Query: 130 IAPELEFYLVDMNK----DPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIYEYC 185 A ELE+YL++ N D + P G + Y I + + + Sbjct: 138 AASELEYYLLENNYREAFDKNYQDLKPAGYY------LEDYHIMQGTRNEHFTSKVRRHL 191 Query: 186 EVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPM 245 + + V+T E G Q E+N + + L +AD+ ++K+ ++E A + TFMAK Sbjct: 192 KKSGVPVETSKGEWGLGQHELNVRYAEILPMADNHVVYKQCLKEVADAMGLSVTFMAKYS 251 Query: 246 EGEPGSAMHMHQSLVDEETGHNLFTGPDG----KPTSLFTSYIAGLQKYTPALMPIFAPY 301 + GS+ H+H SL + G N F G K + LF ++ G KY P +MP +AP Sbjct: 252 TDQAGSSSHIHMSLWKD--GKNAFIGDQVFGPVKGSDLFRWFLGGWIKYVPDVMPFYAPT 309 Query: 302 INSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATLA 361 +NSY+R AP +AW YDNRT GFR+ SG A+ RIE RIPG DCNPYLA AA+LA Sbjct: 310 VNSYKRFVDGSWAPTRLAWSYDNRTAGFRVVGSG-ASLRIECRIPGADCNPYLAFAASLA 368 Query: 362 AGYLGMTQKLEATEPLLSDGYELPY--QLPRNLEEGLTLMGACEPIAEVLGEKFVKAYLA 419 +G G+ K+E D Y + ++P L E + L +E GE+ VK Y Sbjct: 369 SGLAGIKNKIEPPAIFEGDIYAAAHLPRVPYTLAEAIPLFENSTFASEAFGEEVVKHYTH 428 Query: 420 LKETEYEAFFRVISSWERR 438 + E +A+ ++ WER+ Sbjct: 429 FFKQEQKAYNESVTDWERK 447 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: 489 Number of extensions: 19 Number of successful extensions: 6 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: 453 Length adjustment: 33 Effective length of query: 411 Effective length of database: 420 Effective search space: 172620 Effective search space used: 172620 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 24 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