Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate GFF3858 Psest_3928 glutamine synthetase, type I
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__psRCH2:GFF3858 Length = 468 Score = 120 bits (301), Expect = 9e-32 Identities = 119/407 (29%), Positives = 165/407 (40%), Gaps = 64/407 (15%) Query: 66 GVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAIS-----PRRVLRRVLEL 120 G+ DM+ +P T + P+ +PT ++ D V P + PR + +R E Sbjct: 59 GIEASDMILMPVDETAVLDPFTEEPTLILVCDIVE----PSTMQGYDRDPRSIAKRAEEF 114 Query: 121 YKAKGWKPVI--APELEFYLVDMNK---------------------DPDLPLQPPIGRTG 157 K G + PE EF++ D K D D+ G G Sbjct: 115 LKTTGIGDTVFVGPEPEFFIFDQVKFKSDISGSMFKIYSEQGSWMTDQDVEG----GNKG 170 Query: 158 -RPETGRQAYSIEAVNEFDPLFEDIYEYCEVQELEVDTLIHEVGAA-QMEINFMHGDPLK 215 RP + + + + + E L V+ HEV A Q EI + Sbjct: 171 HRPAVKGGYFPVPPCDHDHEIRTAMCNAMEDMGLVVEVHHHEVATAGQNEIGVKFNTLVA 230 Query: 216 LADSVFLFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGK 275 AD V K V A + ATFM KP+ G+ GS MH+H S+ + G N F G Sbjct: 231 KADEVQTLKYCVHNVADAYGKTATFMPKPLYGDNGSGMHVHMSI--SKDGKNTFAGEGYA 288 Query: 276 PTSLFTSY-IAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPH- 333 S Y I G+ K+ AL P NSY+RL AP+ +A+ NR+ RIP+ Sbjct: 289 GLSETALYFIGGIIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYV 348 Query: 334 SGPAARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPLLSDGYELPYQLPRNLE 393 S P ARRIE R P NPYL AA L AG G+ K+ + + Y+LP E Sbjct: 349 SSPKARRIEARFPDPAANPYLCFAALLMAGLDGIQNKIHPGDAADKNLYDLP------PE 402 Query: 394 EGLTLMGACEPIAEVLGE----------------KFVKAYLALKETE 424 EG + C + E L E +F+ AY+ LK E Sbjct: 403 EGKLIPQVCGSLKEALEELDKGRAFLTKGGVFSDEFIDAYIELKSEE 449 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: 509 Number of extensions: 29 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: 468 Length adjustment: 33 Effective length of query: 411 Effective length of database: 435 Effective search space: 178785 Effective search space used: 178785 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