Alignments for a candidate for fadB in Desulfobacter vibrioformis DSM 8776

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Desulfobacter vibrioformis DSM 8776

Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_035235476.1 Q366_RS00865 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= SwissProt::O32178
         (789 letters)



>NCBI__GCF_000745975.1:WP_035235476.1
          Length = 802

 Score =  662 bits (1708), Expect = 0.0
 Identities = 360/810 (44%), Positives = 512/810 (63%), Gaps = 29/810 (3%)

Query: 1   MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60
           M + IRKAAV+GSG+MG GIAA LA  G+ VLLLDIVP DLT +E+K          R+R
Sbjct: 1   MVRKIRKAAVIGSGIMGGGIAALLAGAGVDVLLLDIVPFDLTDKEKK------DPGARNR 54

Query: 61  LSRQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA 120
           + +  M+  L   P+   S K+ S I+ GNL+DD EKL E DWI+EVVVENL++K+ +F 
Sbjct: 55  IVQAGMEAALASNPSLFYSKKDASRISTGNLDDDIEKLSECDWIVEVVVENLKIKRALFE 114

Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180
            V + RK G+IV+SNTSGI +++M+EG S +FK HF+GTHFFNP RY+ LLE+IP  ET 
Sbjct: 115 KVAKVRKEGTIVTSNTSGIPLKDMSEGFSQEFKEHFMGTHFFNPVRYMHLLELIPGAETK 174

Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITG 240
           P+++ F+  FGE  LGKG+V AKDTPNF+ NRIG  G+   ++ ML+    + EVD++ G
Sbjct: 175 PEVMDFIARFGEKNLGKGIVWAKDTPNFVGNRIGVQGIGACIKFMLEDKMTIPEVDALFG 234

Query: 241 PLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE-KEVFRIPSFMNDMLEKGWIGSK 299
           P +GRPK+A F+T D+VG+DT  HVA+N YD  + DE ++   +P F++ M++K  +G+K
Sbjct: 235 PALGRPKTAIFKTTDLVGIDTMLHVAQNSYDLCEDDEQRDTLVLPEFISTMVDKNMLGNK 294

Query: 300 AGQGFYKKE-----GKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDD 354
              GFYK E      K    L+  TL Y +  +   P L  A++    K K+  ++  DD
Sbjct: 295 TRGGFYKTELTPEWKKLRKVLNVDTLEYEDFERASFPCLAEARKKATLKEKLACVLKGDD 354

Query: 355 RAGRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEK 414
           +  +  W   +    Y+A  + EIAD I  ID AMKWG+ +E+GPFE WDA G++Q+ E+
Sbjct: 355 KGAQFAWKCQANAFQYAANRVPEIADTIVEIDNAMKWGYNFEMGPFETWDAYGVEQAVER 414

Query: 415 LEQLGADMPGWIKEMLDKGNETFYIKENGTVFYYD--RGEYRAVKENKKRIHLQALKETK 472
           ++  G D+P  + +ML KG  +FY  ENG  +YYD   GEY+AV  +K  + + A K   
Sbjct: 415 MKSQGLDVPANVTDMLAKGVTSFYKLENGIRYYYDFPAGEYKAVPVSKNMVSIAAAKGNN 474

Query: 473 GVIAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKN 532
             + +N+ A+L+D+GDDV  +EFH+K NAI  +I+  I K L+  E N  GLVIGN+   
Sbjct: 475 KTVFQNASAALVDIGDDVFCIEFHTKMNAINGEIVDSIGKALDYVEENGAGLVIGNEAGG 534

Query: 533 ----FCVGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGT 588
               F  GA+L+ +     D  + E+D  + + Q  + + KY+  PVVAAP+GM LGGG 
Sbjct: 535 MPGAFSAGADLSFVSKLCHDKKYTEIDAFLAKAQAGIQRAKYAPFPVVAAPYGMVLGGGC 594

Query: 589 EACLPAARIQAASEAYMGLVESGVGLIPGGGGNKEL---YINHLR----RGHDPMNAAMK 641
           E CL A RI A +E +MGLVE GVGL+P GGG   L   Y+N L     +  D     ++
Sbjct: 595 ETCLGADRIVAHTELFMGLVEIGVGLLPAGGGCMNLWKKYVNALPGKTVKEVDLAKFFVQ 654

Query: 642 TFETIAMAKVSASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKV 701
            F  IAMA VS SA +AR+   L   D+I +N+D+L+ +AK+    + D G+ PP+K+K+
Sbjct: 655 AFMKIAMAAVSMSAAQARDNGFLGLADRIVMNRDNLVGEAKKEVLKMVDDGYVPPLKKKL 714

Query: 702 KVPGETGYAALLLGAEQMKL--SGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEI 759
           KV G  G    ++ AE   L    ++SE+D  +AK++AYV++GG    G+E+ EE +L++
Sbjct: 715 KVIGNAGQG--MVNAELFNLLNGNFMSEYDAFLAKRIAYVVSGGDANEGSEISEEAILKL 772

Query: 760 EREAFLSLSGEAKSQARMQHMLVKGKPLRN 789
           EREAF+ L  E K+ AR+ HML  GKPLRN
Sbjct: 773 EREAFVDLCREEKTIARIDHMLKTGKPLRN 802


Lambda     K      H
   0.316    0.134    0.382 

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: 1515
Number of extensions: 71
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: 789
Length of database: 802
Length adjustment: 41
Effective length of query: 748
Effective length of database: 761
Effective search space:   569228
Effective search space used:   569228
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 (21.6 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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