Alignments for a candidate for fadB in Rhodomicrobium vannielii ATCC 17100

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Rhodomicrobium vannielii ATCC 17100

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_013418243.1 RVAN_RS02765 3-hydroxyacyl-CoA dehydrogenase

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_000166055.1:WP_013418243.1
          Length = 724

 Score =  425 bits (1092), Expect = e-123
 Identities = 272/722 (37%), Positives = 385/722 (53%), Gaps = 26/722 (3%)

Query: 5   SAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDN 64
           S+ +  V  D IA +TID PG+ MN +  EF  ++   I++   +  ++G+V  S K  +
Sbjct: 2   SSISYQVDADGIATLTIDQPGKSMNVISPEFTEELSEAIERAAADSSVKGIVITSGK-SS 60

Query: 65  FIAGADI----NMIGNCKTAQEAEALARQGQ--QLMAEIHALPIQVIAAIHGACLGGGLE 118
           F+AGAD+     MI + + A  AEAL    +  +++  +  +   V  AI+G  LGGG E
Sbjct: 61  FVAGADLIGMSGMIEHARNAPAAEALKVSSRLTEVLRRLETIGKPVATAINGTALGGGFE 120

Query: 119 LALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQ 178
           +ALA H RV  DD    +G PEVQ+GLLPG+GGTQR+PRLIG+  +  ++L GK L  +Q
Sbjct: 121 IALATHYRVAADDESIKIGQPEVQVGLLPGAGGTQRIPRLIGIMASAPLLLEGKHLSPQQ 180

Query: 179 ALKLGLVDDVVPHSILL-EAAVELAKKERPSSRPLPVRERILAGPLG-----RALLFKMV 232
           A   GL+ DVVP + LL +A   L   +  S +P   R   + G  G      A LF   
Sbjct: 181 AKSSGLIHDVVPAAELLAKAKAWLLSPQAKSVQPWDERGFKVPGGAGGMHPAAAQLFMAA 240

Query: 233 GKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQAL-RSIFF- 290
              T  KT GNYPA + IL  V  G       G   EA+ F  L   P + A+ R++F  
Sbjct: 241 NAMTRDKTLGNYPAAQAILSAVYEGTQVPIDLGLKIEAKYFLSLLRGPVAPAMIRTLFVN 300

Query: 291 ---ASTDVKKDPGSDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINH 347
              A   V++  G   P A    +G+LG G+MG  IAYV A   GI V + D + +    
Sbjct: 301 KGRADKLVRRPQG--VPKAKFKKIGMLGAGMMGAAIAYVAASN-GIEVVLLDRDVEAAER 357

Query: 348 ALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMV 407
              Y+   +E  V RR    ++    LA I  T DY   A  D IIEAVFE+  +K  + 
Sbjct: 358 GKGYARKLVEKAVSRRKTTEADGQGLLARIHATADYADLADVDYIIEAVFEDRAIKADVT 417

Query: 408 AEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSA 467
            +VE       IF SNTS++PI  +A  + RPE+ IG+HFFSP EKMPLVEII    TS 
Sbjct: 418 KKVEAVIRPDVIFGSNTSTIPITSLAEASERPEKFIGIHFFSPAEKMPLVEIIRGKKTSD 477

Query: 468 QTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFG 527
           + +A T+   +   KTPIVV D  GF+ +R    YI E   MLT+G     ++ A    G
Sbjct: 478 EALAVTLDFVQAIRKTPIVVNDGRGFFTSRFCMNYIGEGEIMLTEGIPAALVENAGKLAG 537

Query: 528 FPVGPIQLLDEVGIDTGTKIIPVLEAAYGERF--SAPANVVSSI-LNDDRKGRKNGRGFY 584
            PVGP+ L DE  ID G KI    E   G+ +  SA   V+ ++ + + R GRKNG+GFY
Sbjct: 538 MPVGPLALADETAIDLGWKIHKAAETDLGDAYTPSAAIGVMEAMYVKNGRAGRKNGKGFY 597

Query: 585 LYGQKGRKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRD 644
            Y + G K+       ++P+        I    + +R +     +AVR +++ V+    D
Sbjct: 598 EYPEGGPKTLWAGLADLFPVKPESEWPSID--DLKKRLLFAQALDAVRTMEDGVLTDPED 655

Query: 645 GDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGES 704
           GD+G +FG+GF P+ GGP   +D +G    VA  +RLA +YG RF+P + L +M A G +
Sbjct: 656 GDVGGIFGLGFAPYTGGPLSMLDGIGIANAVAECERLAARYGERFSPPKLLRDMAAEGRT 715

Query: 705 FW 706
           F+
Sbjct: 716 FY 717


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: 1006
Number of extensions: 45
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: 724
Length adjustment: 40
Effective length of query: 674
Effective length of database: 684
Effective search space:   461016
Effective search space used:   461016
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