Alignments for a candidate for ech in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Sulfuritalea hydrogenivorans DSM 22779

Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate WP_041097743.1 SUTH_RS05635 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_000828635.1:WP_041097743.1
          Length = 697

 Score =  189 bits (481), Expect = 3e-52
 Identities = 133/399 (33%), Positives = 207/399 (51%), Gaps = 26/399 (6%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSL-KEGV 60
           +V VIG+G MG GI      AG  V M ++  E L + +  I+ +     + G L +E +
Sbjct: 299 RVGVIGAGTMGGGITMNFLNAGIPVTMLEMKQEALDKGIATIRKNYENSMKKGKLTQEKL 358

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
           +Q +  +   T      K +D +IEAV E++ +K  +F+  +A A P A+LA+NTS+L +
Sbjct: 359 DQRMGMLSG-TLSYDDFKDADLIIEAVFEEISVKEAVFKQLDAIAKPGAILASNTSTLDV 417

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
           ++IA+  K PQ VVGMHFF+P  +M L+E+VRG  T+ +V+ T  ++AK + K  +V   
Sbjct: 418 NKIANFTKRPQDVVGMHFFSPANVMKLLEVVRGAATAKDVMATVMQVAKKIKKTAVVSGV 477

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240
             GF  NR++        +L+E+G A+  +VD  A+E+ G  MG F + D  G DIG+++
Sbjct: 478 CDGFIGNRMIEHYGRVAGFLLEEG-ATPAQVD-KALEKWGMAMGPFRMGDLAGNDIGWAI 535

Query: 241 WKAVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPS------PGKFVRPTLPSTSKK 294
            K               +KL  QG+ G K+G G+Y Y        P   V   L +  K+
Sbjct: 536 RKRRYVEKPSIRYAKFADKLCEQGRYGQKTGKGWYLYQPGNRKAIPDPEVDTMLEAYRKE 595

Query: 295 LG------------RYLISPAVNEVSYLLREGIVGK-DDAEKGCVLGLGLP---KGILSY 338
           LG            +  I   VNE + +L EGI  +  D +   + G G P    G + Y
Sbjct: 596 LGITPRKISDAEIVQRCIYALVNEGARILEEGIAARASDIDMIYLTGYGFPLHRGGPMLY 655

Query: 339 ADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           ADE+G+  V  +++E   TSG   + P PL+   V +GK
Sbjct: 656 ADEVGLYNVARSMKEFAATSGDAFWEPAPLIAKRVADGK 694



 Score = 99.4 bits (246), Expect = 5e-25
 Identities = 67/193 (34%), Positives = 95/193 (49%), Gaps = 9/193 (4%)

Query: 408 AWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLT 467
           A I L+ P   N +  D+   I   +D       V+ + + G  R FS GAD+ EFGS  
Sbjct: 13  AVITLDNPP-VNGLGYDLRCGIVAGIDQATADPAVKAVVLIGSDRAFSGGADIREFGS-- 69

Query: 468 PVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPEI 527
                 A      V   ++   KPV+A I G+ +GGG+EL L   FRVA   A +  PEI
Sbjct: 70  --PKSYAEPNLLTVIRIVEACPKPVVAAIGGVCMGGGLELTLGCHFRVAIAGASIALPEI 127

Query: 528 NLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAE---PEELESEV 583
            LGL+PG GGTQR+ R+ G    L L+L+G  V +E+     + +   E    + L+  +
Sbjct: 128 KLGLLPGAGGTQRMPRIVGVEAALNLILSGNPVPSEKFKGTPLFDEFIEGNGGDLLKGAL 187

Query: 584 RKLANAIAEKSPL 596
                 +AEK PL
Sbjct: 188 AFADKVVAEKRPL 200


Lambda     K      H
   0.316    0.134    0.377 

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: 959
Number of extensions: 46
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 651
Length of database: 697
Length adjustment: 39
Effective length of query: 612
Effective length of database: 658
Effective search space:   402696
Effective search space used:   402696
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: 54 (25.4 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