GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Shewanella sp. ANA-3

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 7022769 Shewana3_0024 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= BRENDA::Q64428
         (763 letters)



>FitnessBrowser__ANA3:7022769
          Length = 716

 Score =  373 bits (958), Expect = e-107
 Identities = 249/727 (34%), Positives = 373/727 (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  TEFLGLFAQDDAVLLSWIEQANAVFNKLEDLPFPTASAIKGFALGGGCETILATDFRIA- 129

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

Query: 223 DPLGPGIKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQV 282
            P             E LE  A+   K     K+  +  +    K++   +T+P +   +
Sbjct: 189 AP-------------EALEAAAIQMLKDAVAEKLDWQARR--QRKMSP--LTLPKLEAMM 231

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

Query: 342 LYNGQVLCK--KNKFGAPQKTVQQLAILGAGLMGAGIAQVSVDKGLKTLLKDTTVTGLGR 399
           ++    L K    K G   K V+  A+LGAG+MG GIA  S  KG   ++KD     L  
Sbjct: 292 IFLNDQLVKGKAKKAGKLAKDVKSAAVLGAGIMGGGIAYQSASKGTPIVMKDIAQPALDL 351

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

Query: 460 KEVESVTPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSK 519
            EVE    E  I ASNTS + IN +A   ++PE+  GMH+F+PV KM L+E+I  + +S+
Sbjct: 412 AEVEQYVSEDAIIASNTSTISINLLAKSMKKPERFCGMHFFNPVHKMPLVEVIRGEHSSE 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: 1156
Number of extensions: 65
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