Alignments for a candidate for acs in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Phaeobacter inhibens BS107

Align Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized)
to candidate GFF1184 PGA1_c11990 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>FitnessBrowser__Phaeo:GFF1184
          Length = 542

 Score =  513 bits (1321), Expect = e-150
 Identities = 275/556 (49%), Positives = 345/556 (62%), Gaps = 21/556 (3%)

Query: 8   DIDDLPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADR 67
           D   L K  ANY  LTPL  L RAA V     +V++G+   T+   YDRC RLASALA  
Sbjct: 6   DESGLEKTAANYVPLTPLSHLRRAAHVFADVPAVVYGNHRKTYAAYYDRCTRLASALAGM 65

Query: 68  SIGPGSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQ 127
            + PG  VA + PN+PA  EAHFGVP CGAVLN +N RL+  TVA++  H ++ V++VD 
Sbjct: 66  GVRPGEVVATLIPNLPAQAEAHFGVPACGAVLNTINTRLDVSTVAYIFDHGEAKVVLVDS 125

Query: 128 EFFTLAEDSLRLMEEKAGSSFKRPLLIVIGDHTCA-PESLNRALSKGAIEYEDFLATGDP 186
           +F TLAE      E KA      PL+I + D   + P S    +      YED LA    
Sbjct: 126 QFLTLAE------EAKAACDGLGPLIIEVPDDQASYPASGRHPI------YEDILAAAAH 173

Query: 187 NYPWQPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLP 246
           ++ W  P DEW+S+AL YTSGTT  PKGVV HHRGAY+M +   + W M     YL  +P
Sbjct: 174 DFDWIMPQDEWESLALNYTSGTTGRPKGVVYHHRGAYLMTMGTVISWRMVMQPKYLAIVP 233

Query: 247 MFHCNGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKED 306
           +FHCNGW   W + VL GT IC R +TA  +Y  IA    THF  AP+VLN +VNA +ED
Sbjct: 234 LFHCNGWNHTWMMPVLGGTLICCRDITAPAIYGAIADEGATHFGGAPIVLNMLVNAAEED 293

Query: 307 TILPLPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPE-WDSLP 365
                 HTV V TAGA P P+ L  +   GF V   YGL+ETYG  T C WK + WD+L 
Sbjct: 294 R-RQFDHTVEVFTAGAPPAPATLEKIEALGFHVTQVYGLTETYGHVTECLWKGDSWDTLD 352

Query: 366 PETQAKLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEAN 425
            + +A + ARQGV +  M+ + V+     + +  +G+  GEIV RGN VMKGYLKNP+A 
Sbjct: 353 QQGRAAIKARQGVAFPMMDHITVMRDDM-QQIAMNGQDQGEIVMRGNSVMKGYLKNPDAT 411

Query: 426 KETFAGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASV 485
            E F GG+FHSGDIAV+HPD YI+I DR+KD+IISGGENISSVEVE V+  HP V  A+V
Sbjct: 412 AEAFQGGYFHSGDIAVQHPDGYIQIADRAKDIIISGGENISSVEVEGVLMGHPDVNLAAV 471

Query: 486 VARPDERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTA 545
           VA+PD++W E PCAFV LK             D+++F RE L  +  PK VVF  LPKT+
Sbjct: 472 VAKPDDKWGEVPCAFVELKPGATVD-----PADLIRFARETLAGFKAPKQVVFQELPKTS 526

Query: 546 TGKIQKHILRTKAKEM 561
           TGKIQK  LR +AK +
Sbjct: 527 TGKIQKFELRQQAKAL 542


Lambda     K      H
   0.319    0.134    0.422 

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: 885
Number of extensions: 38
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: 569
Length of database: 542
Length adjustment: 36
Effective length of query: 533
Effective length of database: 506
Effective search space:   269698
Effective search space used:   269698
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources