Alignments for a candidate for fadB in Ochrobactrum thiophenivorans DSM 7216

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Ochrobactrum thiophenivorans DSM 7216

Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate WP_094508199.1 CEV31_RS15760 enoyl-CoA hydratase/isomerase family protein

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_002252445.1:WP_094508199.1
          Length = 738

 Score =  429 bits (1102), Expect = e-124
 Identities = 265/725 (36%), Positives = 397/725 (54%), Gaps = 29/725 (4%)

Query: 7   FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66
           F +    D IA++T D+P + MN    E   ++ AII     +++++GVV  S K D F 
Sbjct: 6   FKVETDADGIALVTWDMPEKSMNVFTVEAMQELNAIIDATTADEKVKGVVITSGK-DTFS 64

Query: 67  AGADINMIGNC---------KTAQEA-----EALARQGQQLMAEIHALPIQVIAAIHGAC 112
            GAD+ M+            K +Q A     + + R G  L  ++       ++AI+G C
Sbjct: 65  GGADLTMLEGMFKEFQKQKVKDSQAAVQSLFDNVGRMGG-LFRKLETSGKPWVSAINGTC 123

Query: 113 LGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGK 172
           +GG  E++LACH RV +D P   +GLPEV++GL PG+GGTQR+PRL     AL+M+ TG 
Sbjct: 124 MGGAFEMSLACHARVASDAPGVKMGLPEVKVGLFPGAGGTQRVPRLANQQDALQMMTTGS 183

Query: 173 QLRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAG----PLGRALL 228
            L A++A  +GLV +V P   L+E A +L K      +P   +   L G        A L
Sbjct: 184 SLTAQRAKAMGLVTEVAPAKKLVETAKKLIKSGLKPVQPWDEKGFKLPGGAIYSAAGANL 243

Query: 229 FKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQS-QALRS 287
           +         +T GNYPA   IL  V  GL     +G   E R F E+  T ++   +RS
Sbjct: 244 WPAATAILRRETSGNYPAALAILRSVYEGLLVPFDTGLKIEQRYFTEILQTTEAGMMIRS 303

Query: 288 IFFASTDVKKDPGS--DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGI 345
           +F +  ++ K      D  P     +G++G G MG GIAYVTA KAGIPV + D + +  
Sbjct: 304 LFVSLQELNKGARRPVDEKPNKFKKIGVIGAGFMGAGIAYVTA-KAGIPVVLIDRDQESA 362

Query: 346 NHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQ 405
           +    ++ + +  ++++     ++++K L+LI+ T DY      DL+IEAVFE+ E+K+ 
Sbjct: 363 DKGKAHTAELVTKEMQKGRATEADKEKLLSLITATPDYSLLEGADLVIEAVFEDREVKRV 422

Query: 406 MVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGT 465
              + E+   A  IFASNTS+LPI  +A  + RP+  IG+HFFSPV+KM LVE+I    T
Sbjct: 423 ATEKAEEVLKATAIFASNTSTLPISGLAKVSKRPKNFIGIHFFSPVDKMLLVEVILGKKT 482

Query: 466 SAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVK 525
           S + +A  +   +   KTPIVV D  GFYVNR +  Y++EA  ML +G     I+ A   
Sbjct: 483 SDKALAVALDYVRAIKKTPIVVNDTRGFYVNRCVLRYMSEAYNMLVEGVPAAMIENAARM 542

Query: 526 FGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFSAPANV--VSSILND-DRKGRKNGRG 582
            G PVGP+ L DE  ID   KI+    A  GE+   P +V  V  ++N+ DRKGRKNG+G
Sbjct: 543 AGMPVGPLALNDETAIDLSQKILKATLADLGEKAVDPRHVELVDKLVNEFDRKGRKNGKG 602

Query: 583 FYLYGQKGRKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSV 642
           FY Y  K   +KK + P +  L   Q   +I   ++ ER ++ +  EA R ++E ++   
Sbjct: 603 FYEYPAK--PAKKHLWPGLKDLYPQQDPDKIDVNELKERFLVTIALEAARVMEEGIVTDP 660

Query: 643 RDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARG 702
           R+ D+G++   GF P+ GG   YID +GA + V + + L  +YG +F   + L++M   G
Sbjct: 661 READVGSILAFGFAPYTGGTLSYIDGMGAKKFVKLAKELQRKYGQQFKAPKLLLDMAESG 720

Query: 703 ESFWK 707
           ESF++
Sbjct: 721 ESFYQ 725


Lambda     K      H
   0.319    0.137    0.393 

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: 961
Number of extensions: 35
Number of successful extensions: 8
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: 714
Length of database: 738
Length adjustment: 40
Effective length of query: 674
Effective length of database: 698
Effective search space:   470452
Effective search space used:   470452
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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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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
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