Alignments for a candidate for fadA in Brucella microti CCM 4915

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Brucella microti CCM 4915

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_004689079.1 BMI_RS13750 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q64428
         (763 letters)



>NCBI__GCF_000022745.1:WP_004689079.1
          Length = 738

 Score =  353 bits (905), Expect = e-101
 Identities = 246/750 (32%), Positives = 378/750 (50%), Gaps = 53/750 (7%)

Query: 40  HINYGVKGD---VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPG 96
           ++N+ V+ D   +A++  + P   +N    +   E   +++ + A+D+I+  V+ S K  
Sbjct: 3   YVNFKVETDADGIALVTWDMPEKSMNVFTVDAMQELNAIIDAVIADDKIKGVVITSGKE- 61

Query: 97  CFVAGADINMLASCTTPQEAARISQ-EG------------QKMFEKLEKSPKPVVAAISG 143
            F  GAD+ ML       +  ++   EG              +F KLE   KP V+AI+G
Sbjct: 62  TFSGGADLTMLEGMFKEFQKQKVKDPEGAVQTLFDNVGKMSGLFRKLETCGKPWVSAING 121

Query: 144 SCLGGGLELAIACQYRIATKDRKTVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLT 203
           +C+GG  E+++AC  R+A+      + +PEV +G+ PGAGGTQR+P++     A  MM T
Sbjct: 122 TCMGGAFEMSLACHARVASDAPGVKMALPEVKVGLFPGAGGTQRVPRLANQQDALQMMTT 181

Query: 204 GRNIRADRAKKMGLVDQLVDPLGPGIKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKG 263
           G ++ A RAK MGLV ++         +P ++ +E     A    KG   + V     KG
Sbjct: 182 GSSLTAQRAKAMGLVTEI---------APAKKLVE----TAKKLIKG-GLKPVQPWDEKG 227

Query: 264 LMEKLTSYAMTIPFVRQQVYKTVEEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAE 323
              KL   A+        ++      ++++T G YPA L I+ +V  GL    D G   E
Sbjct: 228 F--KLPGGAI-YSAAGANLWPAATAILRRETSGNYPAALAILKSVYEGLLVPFDTGLKIE 284

Query: 324 SEKFGELALTKESKALMG--LYNGQVLCKKNKFGAPQKT--VQQLAILGAGLMGAGIAQV 379
              F E+  T E+  ++     + Q L K  +    +K   ++++ ++GAG MGAGIA V
Sbjct: 285 QRYFTEILQTTEAGMMIRSLFVSLQELNKGARRPVDEKPTRLKKIGVIGAGFMGAGIAYV 344

Query: 380 SVDKGLKTLLKDTTVTGLGRGQQQVFKGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFE 439
           +   G+  +L D       +G+      +  +++K   T  +++ + S +    DY   E
Sbjct: 345 TAKAGIPVVLIDRDQESADKGKAHTADLITKEMQKGRATEADKEKLLSLITATPDYAQLE 404

Query: 440 KADMVIEAVFEDLAVKHKVLKEVESVTPEHCIFASNTSALPINQIAAVSQRPEKVIGMHY 499
            AD+VIEAVFED  VK    ++ E V     +FASNTS LPI  +A VS+RP+  IG+H+
Sbjct: 405 GADLVIEAVFEDREVKRVATEKAEEVLKSSAVFASNTSTLPITGLAKVSKRPKNFIGIHF 464

Query: 500 FSPVDKMQLLEIITTDKTSKDTTASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVI 559
           FSPVDKM L+E+I   KTS    A A+       K  IVV D  GFY  RC+   MSE  
Sbjct: 465 FSPVDKMMLVEVILGKKTSDKALAVALDYVRAIKKTPIVVNDTRGFYVNRCVLRYMSEAY 524

Query: 560 RILQEGVDPKKLDALTTGFGFPVGAATLADEVGIDVAQHVAE----DLG-KAFGERFGGG 614
            +L EGV    ++      G PVG   L DE  ID++Q + +    DLG KA   R    
Sbjct: 525 NMLVEGVPAAMIENAARMAGMPVGPLALNDETAIDLSQKILKATLADLGPKAVDPR---- 580

Query: 615 SVELLKLMVSK-GFLGRKSGKGFYIYQSGSKNKNLNSEIDNILVNLRLPAKPEVSSDEDI 673
            VEL+  +V++    GRK+GKGFY Y +    K+L       L +L     P+    +++
Sbjct: 581 HVELVDKLVNEFDRKGRKNGKGFYDYPAKPAKKHLWPG----LKDLYPQQNPDKIDVKEL 636

Query: 674 QYRVITRFVNEAVLCLQEGILATPEEGDIGAVFGLGFPPCLGGPFRFVDLYGAQKVVDRL 733
           + R +     EA   ++EGI+  P E D+G++   GF P  GG   ++D  GA+K V   
Sbjct: 637 KERFLVTIALEAARVMEEGIVTDPREADVGSILAFGFAPYTGGTLSYIDGMGAKKFVQLA 696

Query: 734 RKYESAYGTQFTPCQLLRDLANNSSKKFYQ 763
           +  +  YG QF   +LL D+A N  + FYQ
Sbjct: 697 KDLQKKYGAQFKAPKLLLDMAEN-GETFYQ 725


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: 1193
Number of extensions: 58
Number of successful extensions: 5
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: 738
Length adjustment: 40
Effective length of query: 723
Effective length of database: 698
Effective search space:   504654
Effective search space used:   504654
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 24 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 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