GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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