Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate RR42_RS28980 RR42_RS28980 fatty acid--CoA ligase
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__Cup4G11:RR42_RS28980 Length = 580 Score = 211 bits (536), Expect = 8e-59 Identities = 159/506 (31%), Positives = 240/506 (47%), Gaps = 35/506 (6%) Query: 58 LAAGLRKSGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTFVARELAYQLQDSG 117 +A L + G+ +GDRV L N +P VF G ++ G I T N + EL Y L DSG Sbjct: 87 IAHALIRDGVTKGDRVALAMRNLPEWPAVFYGALLTGAIVTPLNAWWTGAELEYGLADSG 146 Query: 118 ATYLLCASNSLETGLEAAKQAKLPQSHIFAYDTSIYDGVTNPQKGCAYWSDLLASEEEGA 177 + + L +E LP IY N A SD S+ E Sbjct: 147 SKIAIVDDERLGRIIE-----HLPGCPALE---KIYVSRAN-----APASDARISQLESL 193 Query: 178 AFTWDE-LSTPALSSTTLALN--------YSSGTTGRPKGVEISHRNYV--------ANM 220 T D+ S PAL +A++ Y+SGTTG+PKG +HRN + M Sbjct: 194 IGTPDQWASLPALPVPVVAIDADDDATIFYTSGTTGKPKGALGTHRNATNVAVAAAFSPM 253 Query: 221 LQYCHTASLHPDYKARLERSRWLCFLPMYHAMAQNIFIAAALYRATPVYIMSKFDFVKML 280 P + L +P +H + AL T + +M ++D V+ + Sbjct: 254 RNCLRRGETIPAPDPGAPQKGMLLSVPFFHVTGCMAVLNGALASGTKIVLMRRWDAVRAM 313 Query: 281 EYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPLGREVCEEVEKLWPPG 340 +R R T VP + + +HP ++DLSS+E V G AP E+ +++++P Sbjct: 314 GLIERERCTAAGGVPTIAWQIIEHPERERFDLSSLENVNYGGAPASAELVRRIKEVFPHS 373 Query: 341 KINIKQGWGMTEATCSVTGWNPAE-ISTSASVGELNANCEAKIMFDGVEVKERNSRGELW 399 I GWGMTE + + T + E + S G E K++ GEL Sbjct: 374 APGI--GWGMTETSATFTSHSAEEYVERPESGGPALPIGEMKVVDGRGHSLPTGETGELM 431 Query: 400 VRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMKELIKVKGNQVAP 459 VR NV++GYW +AT +T DGWL TGDIA +D++G ++VDRMK+++ G + Sbjct: 432 VRGANVVRGYWNKPEATAQTFI-DGWLKTGDIARLDEEGFVYIVDRMKDMLIRGGENIYS 490 Query: 460 AELEALLLEHPAISDVAVIGVVINN-DERPRAYVVLRPGQSATANEIAHYLDNKVSAFKR 518 E+E+ L +HPAI D A++G+ E P A V L+PG AT E+ ++ +++AFK Sbjct: 491 IEVESALYDHPAIMDAALVGIPHRTLGEEPAAVVSLKPGAQATEAELQAFVGERLAAFKV 550 Query: 519 ITGGVVFLEAIPKNPSGKILRMKLRE 544 V + +P+N +GKIL+ LR+ Sbjct: 551 PVRIVFCPDMLPRNANGKILKSTLRK 576 Lambda K H 0.319 0.134 0.403 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: 693 Number of extensions: 33 Number of successful extensions: 7 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: 556 Length of database: 580 Length adjustment: 36 Effective length of query: 520 Effective length of database: 544 Effective search space: 282880 Effective search space used: 282880 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 (21.7 bits) S2: 53 (25.0 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