Alignments for a candidate for fadA in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Shewanella oneidensis MR-1

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 199218 SO0021 fatty oxidation complex, alpha subunit (NCBI ptt file)

Query= BRENDA::Q64428
         (763 letters)



>FitnessBrowser__MR1:199218
          Length = 716

 Score =  372 bits (956), Expect = e-107
 Identities = 251/727 (34%), Positives = 374/727 (51%), Gaps = 32/727 (4%)

Query: 45  VKGDVAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADI 104
           ++ ++A +  N+P S VN  ++E  +     ++ I     I++ VL S K   F+ GADI
Sbjct: 13  LEDNIAKLCFNAPGS-VNKFDRETLASLDAALDSIKQQSNIQALVLTSGKD-TFIVGADI 70

Query: 105 NMLASCTTPQEAARIS--QEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIAT 162
                     +A  +S  ++   +F KLE  P P  +AI G  LGGG E  +A  +RIA 
Sbjct: 71  TEFLGLFAQDDAVLLSWVEQANAVFNKLEDLPFPTASAIKGFALGGGCETILATDFRIA- 129

Query: 163 KDRKTVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLV 222
            D    +G+PE  LGI+PG GGT RLP+++G   A + + TG   RA+ A K+G VD +V
Sbjct: 130 -DTTAKIGLPETKLGIIPGFGGTVRLPRVIGADNALEWITTGNEQRAEDALKVGAVDAVV 188

Query: 223 DPLGPGIKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQV 282
            P             E LE  A+   K     K+  +  +    KL+   +T+P +   +
Sbjct: 189 AP-------------EALEVAAIQMLKDAVAEKLDWQARR--QRKLSP--LTLPKLEAMM 231

Query: 283 YKTVEEKVKKQTKGL-YPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMG 341
             T  + +     G  YPAP+  ++ V+    +G       E + F +LA T  +KAL+G
Sbjct: 232 SFTTAKGMVFSVAGKHYPAPMAAVNVVEQAATKGRSDALQIEHQAFIKLAKTDVAKALIG 291

Query: 342 LY-NGQ-VLCKKNKFGAPQKTVQQLAILGAGLMGAGIAQVSVDKGLKTLLKDTTVTGLGR 399
           ++ N Q V  K  K G   K V   A+LGAG+MG GIA  S  KG   ++KD     L  
Sbjct: 292 IFLNDQFVKGKAKKAGKLAKAVNSAAVLGAGIMGGGIAYQSASKGTPIVMKDIAQPALDL 351

Query: 400 GQQQVFKGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVL 459
           G  +  K L+ +V +   T  +   + +N+   L+Y   + AD+V+EAV E   VK +VL
Sbjct: 352 GLNEAAKLLSAQVARGRSTPEKMAKVLNNITPALEYAPVKHADVVVEAVVEHPKVKAQVL 411

Query: 460 KEVESVTPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSK 519
            EVE    E  I ASNTS + I+ +A   ++PE+  GMH+F+PV KM L+E+I  + +S+
Sbjct: 412 AEVEQYVSEDAIIASNTSTISISLLAKSMKKPERFCGMHFFNPVHKMPLVEVIRGEHSSE 471

Query: 520 DTTASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLD-ALTTGF 578
           +T AS VA   K GK  IVV D PGF+  R L P  +    +L EG D   +D  +   F
Sbjct: 472 ETIASVVAYASKMGKTPIVVNDCPGFFVNRVLFPYFAGFNGLLAEGGDFAAIDKVMEKQF 531

Query: 579 GFPVGAATLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYI 638
           G+P+G A L D VG+D   H    + + F +R G    + + +M     LG+K+GKGFY 
Sbjct: 532 GWPMGPAYLLDVVGLDTGHHAQAVMAEGFPDRMGKSGNDAIDVMFENKRLGQKNGKGFYA 591

Query: 639 YQSGSKNKNLNSEIDNILVNLRLPA--KPEVSSDEDIQYRVITRFVNEAVLCLQEGILAT 696
           Y   S+ K    ++D     L   A  + +    ++I  R +   + E V CL+EGI+A+
Sbjct: 592 YSVDSRGKP-KKDVDPTSYELLKAAFGEQKAFDADEIIARTMIPMIIETVRCLEEGIVAS 650

Query: 697 PEEGDIGAVFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQLLRDLANN 756
           P E D+G V+GLGFPP  GG FR++D  G    V    KY +  G  +     +R LA N
Sbjct: 651 PAEADMGLVYGLGFPPFRGGVFRYLDTMGVANFVALADKY-AHLGGLYQVTDAMRALAAN 709

Query: 757 SSKKFYQ 763
           +   +YQ
Sbjct: 710 NG-SYYQ 715


Lambda     K      H
   0.317    0.135    0.380 

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: 1145
Number of extensions: 63
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: 763
Length of database: 716
Length adjustment: 40
Effective length of query: 723
Effective length of database: 676
Effective search space:   488748
Effective search space used:   488748
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: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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 2024 update 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