GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__ANA3:7022769 Shewana3_0024 multifunctional
           fatty acid oxidation complex subunit alpha (RefSeq)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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