Alignments for a candidate for fadB in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadB in Sulfuritalea hydrogenivorans DSM 22779

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_041096229.1 SUTH_RS00440 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_000828635.1:WP_041096229.1
          Length = 720

 Score =  422 bits (1084), Expect = e-122
 Identities = 271/717 (37%), Positives = 385/717 (53%), Gaps = 25/717 (3%)

Query: 11  VRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFIAGAD 70
           V  + IA +  D P +  N L A+        +++   +  ++G+V  SAK D FIAG D
Sbjct: 6   VDAEGIATVEFDYPEKSQNILNAKSMGAYADAMQKALADPAVKGIVVASAKKD-FIAGGD 64

Query: 71  INMIGNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGRVCTD 130
           +  +G    A    A      +LM  I      V AA++G  LGGG+E+AL CH RV  D
Sbjct: 65  LAELGAATDAAAFHASISAWHKLMRAIELGGKPVAAALNGTTLGGGMEVALGCHYRVAAD 124

Query: 131 DPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVDDVVP 190
           +PK   G PEV LGLLPG+GGTQRLPRL G+  A  +++ GK+++A +A K+G++  VV 
Sbjct: 125 NPKARFGFPEVTLGLLPGAGGTQRLPRLAGMMAAAPLLMEGKRIKAAEAQKIGMIHAVVT 184

Query: 191 HSILLEAAVE-----LAKKERPSSRPLPVRERILAG-----PLGRALLFKMVGKKTEHKT 240
                 AA +     LA   +P  +P  ++   + G     P G  +L        E KT
Sbjct: 185 VGAERTAARQWVADTLAAGTKPL-QPWDMKGAKIPGGGPNTPNGMQMLMAANAMLRE-KT 242

Query: 241 QGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQ-ALRSIFFASTDVKKDP 299
             NYPA + IL  V  GL+    +G   EAR F  L M+P S+  +RS+FF   +  K  
Sbjct: 243 CDNYPAPKHILSCVYEGLSTNIDTGLAIEARYFTNLVMSPVSKNMIRSLFFGMQEANKLA 302

Query: 300 GSDA--PPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSWDQLE 357
              A  P    + +G+LG G+MG GIA  TA  AG+ + + D   +       Y+  Q  
Sbjct: 303 SRPAGVPTQKYSKIGMLGAGMMGAGIAMSTAT-AGMAIVLLDTTQEAAEKGKDYARKQWS 361

Query: 358 GKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQ----N 413
            +V +  + A   +  LA I  T DY      +L+IEAVFE  E+K  +  + E     +
Sbjct: 362 KQVAKGRMTADAMEALLARIHPTADYADLKSCELVIEAVFEKREIKADVTKKAEAVLLAD 421

Query: 414 CAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATT 473
            A   IFASNTS+LPI  +A  + RP   IGLHFFSP EKMPLVEII    TS  T+A +
Sbjct: 422 PAPDAIFASNTSTLPITGLAEASARPANFIGLHFFSPAEKMPLVEIIVGKATSDATLARS 481

Query: 474 VKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPI 533
           +   +  GKTPIVV D  GFY +R+   Y++E + +L +G     ID A +  G PVGP+
Sbjct: 482 MDYVRAIGKTPIVVNDSRGFYTSRVFGTYVSEGMALLEEGVPPALIDKAGLIAGMPVGPL 541

Query: 534 QLLDEVGIDTGTKIIPVLEAAYGERF--SAPANVVSSILND-DRKGRKNGRGFYLYGQKG 590
            L DEV I+   KI     A  G  +   A   V + ++ D  R GRK+G GFY Y   G
Sbjct: 542 ALADEVSIELVHKIAQQTRADLGSAYVERAADRVAAKMVADLGRLGRKSGAGFYDYPADG 601

Query: 591 RKSKKQVDPAIYPL-IGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGA 649
            K         +P+ +G  G   ++  Q+ ER +++   E VRC++E+V+R+  D D+GA
Sbjct: 602 PKHLWSGLAQHFPVRVGADGTAALTLEQIVERLILVQSVETVRCLEEKVLRAPIDADVGA 661

Query: 650 VFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGESFW 706
           + G G+PPF GGP  ++ +LG+ + VA + RLA Q G RFTP + L +M ARGE+F+
Sbjct: 662 ILGWGYPPFRGGPIGWLHTLGSAKSVAALDRLAEQNGPRFTPPKLLRDMAARGENFY 718


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: 983
Number of extensions: 36
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: 714
Length of database: 720
Length adjustment: 40
Effective length of query: 674
Effective length of database: 680
Effective search space:   458320
Effective search space used:   458320
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 Apr 09 2024. 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