Aligments for a candidate for fadA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Aligments for a candidate for fadA in Shewanella amazonensis SB2B

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 6935814 Sama_0032 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= BRENDA::Q64428
         (763 letters)



>FitnessBrowser__SB2B:6935814
          Length = 716

 Score =  352 bits (903), Expect = e-101
 Identities = 239/721 (33%), Positives = 368/721 (51%), Gaps = 32/721 (4%)

Query: 49  VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLA 108
           +A +  N+P S VN  ++E  +     ++ +  +D  ++AVL S K   F+ GADI    
Sbjct: 17  IARLCFNAPGS-VNKFDRETLASLNAALDVLKDSDA-KAAVLTSGKD-TFIVGADITEFL 73

Query: 109 SCTTPQEAARISQEGQK--MFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRK 166
           +    ++A  +    Q   +F KLE  P P V+AI G  LGGG E  +A  +R+A  D  
Sbjct: 74  ALFAEEDAKLMEWIAQANVVFNKLEDLPFPTVSAIKGFALGGGCEAILATDFRVA--DTS 131

Query: 167 TVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLG 226
             +G+PE  LG++PG GGT RLP+++G   A + + TG++ R + A K+G +D +V P  
Sbjct: 132 AKIGLPETKLGLIPGFGGTVRLPRLIGADNALEWITTGKDQRPEDALKVGAIDAVVAP-- 189

Query: 227 PGIKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKTV 286
              ++ E   I+ L +         A R  + KQ+   + KL +  M+    +  VY   
Sbjct: 190 ---ENLEAAAIQMLNDALAGKLDWQARR--ARKQAPLTLPKLEAM-MSFTTAKGMVYAVA 243

Query: 287 EEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNGQ 346
            +         YPAP+  +  V+           + E   F +LA T  + AL+G++   
Sbjct: 244 GKH--------YPAPMAAVSVVEQAAGMSRAEALVVEHNAFIKLAKTDVATALIGIFLND 295

Query: 347 VLCK--KNKFGAPQKTVQQLAILGAGLMGAGIAQVSVDKGLKTLLKDTTVTGLGRGQQQV 404
            L K    K     K ++  A+LGAG+MG GIA  S  KG   ++KD     L  G  + 
Sbjct: 296 QLVKGKAKKASKLAKDIKHAAVLGAGIMGGGIAYQSASKGTPIVMKDINQAALDLGVNEA 355

Query: 405 FKGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEVES 464
            K L+ +V +   T  +   + +N+   LDY   +  ++V+EAV E+  VK  VL +VE+
Sbjct: 356 AKLLSAQVARGRSTPDKMAKVLNNITPALDYAPLKDVNVVVEAVVENPKVKAMVLADVEN 415

Query: 465 VTPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTTAS 524
           V  +  I ASNTS + I+ +A   + P +  GMH+F+PV KM L+E+I    TS++T AS
Sbjct: 416 VVADDAIIASNTSTISIDLLAKSLKNPARFCGMHFFNPVHKMPLVEVIRGKDTSEETVAS 475

Query: 525 AVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLD-ALTTGFGFPVG 583
            VA   K GK  IVV D PGF+  R L P  +    +L +G D   +D  +   FG+P+G
Sbjct: 476 VVAYASKMGKTPIVVNDCPGFFVNRVLFPYFAGFNGLLADGGDFAAIDKVMEKQFGWPMG 535

Query: 584 AATLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIY---Q 640
            A L D VG+D   H    +   F +R G    + + +M   G LG+K+GKGFY Y   +
Sbjct: 536 PAYLLDVVGLDTGHHAQAVMADGFPDRMGKSDKDAIDVMYEAGRLGQKNGKGFYQYSIDK 595

Query: 641 SGSKNKNLNSEIDNILVNLRLPAKPEVSSDEDIQYRVITRFVNEAVLCLQEGILATPEEG 700
            G   K+++     +L      A+    +DE I  R +   + E V CL+EGI+A+P E 
Sbjct: 596 RGKPKKDVDPASYTMLAE-AFGAQKAFEADEIIA-RTMIPMIIETVRCLEEGIVASPAEA 653

Query: 701 DIGAVFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQLLRDLANNSSKK 760
           D+G V+GLGFPP  GG FR++D  G    V    KY +  G  +     +R+LA+N+   
Sbjct: 654 DMGLVYGLGFPPFRGGVFRYLDTMGVANFVALADKY-AHLGGLYQVTDAMRELASNNGSY 712

Query: 761 F 761
           +
Sbjct: 713 Y 713


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: 1128
Number of extensions: 71
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 Sep 17 2021. 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 paper from 2022 on GapMind for carbon sources, or view the source code.

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