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_041096201.1 SUTH_RS00350 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_000828635.1:WP_041096201.1
          Length = 653

 Score =  184 bits (467), Expect = 1e-50
 Identities = 118/333 (35%), Positives = 185/333 (55%), Gaps = 16/333 (4%)

Query: 3   VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERI-KWSLSKLRESGSLKEGVE 61
           V V+G+GVMG  IA   A+ G  V + D S E +  A+ R  K+   KLR+    +  ++
Sbjct: 315 VHVVGAGVMGGDIAAWCALRGMTVTLQDQSVERIAPAVGRAAKFFEKKLRDRKLARFALD 374

Query: 62  QVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPIS 121
           +++A       +   ++ +D +IEA+ E+LE K+ +F + EA A P A+LA+NTSSL ++
Sbjct: 375 RLIA-----DPRGDGVRQADVIIEAIFENLEAKQALFADIEARAKPEALLASNTSSLKLA 429

Query: 122 EIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDV 181
           +IA+  K P R+VG+HFFNP  +MPLVE+V G  T+ E  +  A   + ++K  + VKD 
Sbjct: 430 DIAAKFKDPSRLVGIHFFNPVAMMPLVEVVAGAGTAPEAAQKAAAFVRKIDKLPLPVKDA 489

Query: 182 PGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVW 241
           PGF VN VL   M      V++GIA   E   +A+   G PMG   LAD  GLD+  +  
Sbjct: 490 PGFLVNAVLAPYMNEAMKCVDEGIA--PETIDAAMLAFGMPMGPIELADTVGLDVAVAAG 547

Query: 242 KAVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGKFVRPTL---PSTSKKLGRY 298
           + +      A P     +LV   KLG KSG G+Y +   GK  +  +    + ++ L + 
Sbjct: 548 RQLVG---DANPPQKLVELVEGKKLGKKSGQGFYTW-IDGKAQKSKVGAGDTANQALAQR 603

Query: 299 LISPAVNEVSYLLREGIVGKDD-AEKGCVLGLG 330
           LI+P ++    L+++G+V   + A+ G + G G
Sbjct: 604 LITPLLDATQRLVKDGVVADAELADAGVIFGTG 636



 Score = 92.4 bits (228), Expect = 6e-23
 Identities = 53/185 (28%), Positives = 101/185 (54%), Gaps = 5/185 (2%)

Query: 407 LAWIVLNRP-TRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEF-G 464
           +AW +L+   +  N +  D++ E+   LD   +     +I  + +   F AGA++ EF  
Sbjct: 18  VAWAILDTADSSTNTLGADVMAELGLILDECAKHPPKGLIFTSAKEAGFIAGANIEEFVA 77

Query: 465 SLTPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVA--SKTAEM 522
           S TP KA+   ++  +++ ++  ++ P +A++ G  +GGG ELAL+  +R+A        
Sbjct: 78  SDTPEKALALVKRGWDLYNRLAAVSYPTLALVRGHCMGGGTELALACRYRIAVDEPGTRF 137

Query: 523 GQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAEPEELES 581
             PE+ LG++PG GG  RL ++ G     +++LTG+ + A+ A ++G+ +    P  +E+
Sbjct: 138 ALPEVMLGIVPGWGGMLRLPQIVGPAAAFDMMLTGKNIDAKRAKKMGLADECLPPRVMEN 197

Query: 582 EVRKL 586
             R L
Sbjct: 198 AARML 202



 Score = 53.5 bits (127), Expect = 3e-11
 Identities = 31/101 (30%), Positives = 55/101 (54%), Gaps = 7/101 (6%)

Query: 299 LISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQTS 358
           +++P +NE    + EGI    +     +L  G+P G +  AD +G+DV V    ++    
Sbjct: 497 VLAPYMNEAMKCVDEGIA--PETIDAAMLAFGMPMGPIELADTVGLDVAVAAGRQL---- 550

Query: 359 GMDHYSPDPLLLSMVKEGKLGRKSGQGFHTYAHEEAKYSTI 399
            +   +P   L+ +V+  KLG+KSGQGF+T+   +A+ S +
Sbjct: 551 -VGDANPPQKLVELVEGKKLGKKSGQGFYTWIDGKAQKSKV 590


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: 878
Number of extensions: 36
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: 3
Length of query: 651
Length of database: 653
Length adjustment: 38
Effective length of query: 613
Effective length of database: 615
Effective search space:   376995
Effective search space used:   376995
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