Alignments for a candidate for prpE in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_1726 3-methylmercaptopropionyl-CoA ligase (DmdB)

Query= SwissProt::M4IS88
         (568 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1726
          Length = 540

 Score =  600 bits (1548), Expect = e-176
 Identities = 293/546 (53%), Positives = 373/546 (68%), Gaps = 21/546 (3%)

Query: 17  NYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGLGSTVAV 76
           N+TALTPL F+ER A+V+P   +VIHGS   TW  TY RCR+ ASAL    IG   TVAV
Sbjct: 14  NHTALTPLSFIERTASVYPDYPAVIHGSIRRTWADTYRRCRRLASALAGRGIGKNDTVAV 73

Query: 77  IAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFSLAEEAL 136
           + PN+PA+ EAHF VPM GAV+N +N+RL+A  IAF+L H  A  ++ D+EF  + + A+
Sbjct: 74  MLPNIPAMLEAHFGVPMIGAVLNALNVRLDAEAIAFMLAHGEAKVLIADREFHDVVQAAI 133

Query: 137 KILAQESKSHYKPPLLVVIGDESCDPKTLEYA--LKTGAIEYEKFLEGGDPEFDWKPPED 194
            +L         PPL++ + D        EY        ++YE FL  GDP+F W+ P+D
Sbjct: 134 GMLDH-------PPLVIDLDDP-------EYGEGQAVSELDYEAFLAEGDPDFAWQWPDD 179

Query: 195 EWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHCNGWCY 254
           EWQ+ISL YTSGTT +PKGVV  HRGAYL SL   + W +    +YLWTLPMFHCNGWCY
Sbjct: 180 EWQAISLNYTSGTTGNPKGVVYHHRGAYLNSLGNQMTWAMGNHPVYLWTLPMFHCNGWCY 239

Query: 255 TWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPLPHLV 314
            W + A  G ++ LR+V  + + + I ++ +TH C AP+VLN +VN P + A   + H V
Sbjct: 240 PWTVTALAGVHVFLRRVDPQKILNLIREHQITHLCGAPIVLNALVNMP-DSAKAAIDHPV 298

Query: 315 HVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQARLNAR 374
             M AGAAPP  V+ A+ E G KV H YGL+E YGP T+CAW   WD LP  ++A++ AR
Sbjct: 299 SAMVAGAAPPAKVIGAVEEMGIKVTHVYGLTEVYGPVTLCAWHAAWDELPLEQRAQIKAR 358

Query: 375 QGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFADGWFH 434
           QGVRY  LEGL V D +T++P P DG T+GEI MRGN VMKGYLKNP A  E+F  GWFH
Sbjct: 359 QGVRYPTLEGLMVADPRTLEPTPHDGQTIGEIFMRGNTVMKGYLKNPSATAEAFEGGWFH 418

Query: 435 SGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDERWGE 494
           +GDLAV H DGY+EI+DR KDIIISGGENIS++E+E  LY HPAVLE +VVARPDE+WGE
Sbjct: 419 TGDLAVTHADGYVEIRDRLKDIIISGGENISTIELEGVLYRHPAVLEAAVVARPDEKWGE 478

Query: 495 SPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKIQKHVLR 554
           +PCAF+TLK      +  V   +II FC+  +  + VP++VVF  LPKT+TGKIQK VLR
Sbjct: 479 TPCAFITLK----SDHTDVREAEIISFCREHLAGFKVPRTVVFTQLPKTSTGKIQKFVLR 534

Query: 555 AKAKEM 560
             AK +
Sbjct: 535 DMAKNL 540


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: 870
Number of extensions: 32
Number of successful extensions: 4
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: 540
Length adjustment: 36
Effective length of query: 532
Effective length of database: 504
Effective search space:   268128
Effective search space used:   268128
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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Protein sequences (fasta format)
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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