Alignments for a candidate for prpE in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Phaeobacter inhibens BS107

Align Acetate--CoA ligase CCL3; HlCCL3; 2-methylbutanoate--CoA ligase CCL4; 2-methylpropanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Hexanoate--CoA ligase CCL3; Isovalerate--CoA ligase CCL3; Pentanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.1; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate GFF1184 PGA1_c11990 acyl-CoA synthetase

Query= SwissProt::M4IS88
         (568 letters)



>FitnessBrowser__Phaeo:GFF1184
          Length = 542

 Score =  490 bits (1262), Expect = e-143
 Identities = 263/555 (47%), Positives = 342/555 (61%), Gaps = 19/555 (3%)

Query: 7   DIDDLPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNH 66
           D   L K AANY  LTPL  L RAA V     +V++G+   T+   Y RC + ASAL   
Sbjct: 6   DESGLEKTAANYVPLTPLSHLRRAAHVFADVPAVVYGNHRKTYAAYYDRCTRLASALAGM 65

Query: 67  SIGLGSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQ 126
            +  G  VA + PN+PA  EAHF VP  GAV+N +N RL+ ST+A++  H  A  V+VD 
Sbjct: 66  GVRPGEVVATLIPNLPAQAEAHFGVPACGAVLNTINTRLDVSTVAYIFDHGEAKVVLVDS 125

Query: 127 EFFSLAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPE 186
           +F +LAEEA     + +     P ++ V  D++  P +  + +      YE  L     +
Sbjct: 126 QFLTLAEEA-----KAACDGLGPLIIEVPDDQASYPASGRHPI------YEDILAAAAHD 174

Query: 187 FDWKPPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPM 246
           FDW  P+DEW+S++L YTSGTT  PKGVV  HRGAYLM++   + W +     YL  +P+
Sbjct: 175 FDWIMPQDEWESLALNYTSGTTGRPKGVVYHHRGAYLMTMGTVISWRMVMQPKYLAIVPL 234

Query: 247 FHCNGWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEA 306
           FHCNGW +TW M    GT IC R +TA  +Y AIA  G THF  AP+VLN +VNA  E+ 
Sbjct: 235 FHCNGWNHTWMMPVLGGTLICCRDITAPAIYGAIADEGATHFGGAPIVLNMLVNAAEEDR 294

Query: 307 IIPLPHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPE-WDSLPP 365
                H V V TAGA P P+ L  +   GF V   YGL+ETYG  T C WK + WD+L  
Sbjct: 295 R-QFDHTVEVFTAGAPPAPATLEKIEALGFHVTQVYGLTETYGHVTECLWKGDSWDTLDQ 353

Query: 366 IKQARLNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANE 425
             +A + ARQGV +  ++ + V+    M+ +  +G   GEIVMRGN+VMKGYLKNP A  
Sbjct: 354 QGRAAIKARQGVAFPMMDHITVM-RDDMQQIAMNGQDQGEIVMRGNSVMKGYLKNPDATA 412

Query: 426 ESFADGWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVV 485
           E+F  G+FHSGD+AV+HPDGYI+I DR+KDIIISGGENISS+EVE  L  HP V   +VV
Sbjct: 413 EAFQGGYFHSGDIAVQHPDGYIQIADRAKDIIISGGENISSVEVEGVLMGHPDVNLAAVV 472

Query: 486 ARPDERWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTAT 545
           A+PD++WGE PCAFV LKP        V   D+I+F +  +  +  PK VVF  LPKT+T
Sbjct: 473 AKPDDKWGEVPCAFVELKP-----GATVDPADLIRFARETLAGFKAPKQVVFQELPKTST 527

Query: 546 GKIQKHVLRAKAKEM 560
           GKIQK  LR +AK +
Sbjct: 528 GKIQKFELRQQAKAL 542


Lambda     K      H
   0.318    0.134    0.415 

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: 884
Number of extensions: 27
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: 568
Length of database: 542
Length adjustment: 36
Effective length of query: 532
Effective length of database: 506
Effective search space:   269192
Effective search space used:   269192
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis