Alignments for a candidate for ech in Limnohabitans curvus MWH-C5

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Limnohabitans curvus MWH-C5

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_108402728.1 B9Z44_RS14150 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_003063475.1:WP_108402728.1
          Length = 699

 Score =  194 bits (492), Expect = 1e-53
 Identities = 134/399 (33%), Positives = 204/399 (51%), Gaps = 26/399 (6%)

Query: 3   VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVEQ 62
           V VIG+G MG GIA     AG  V M +   E L + +  I+ +     + G LKE    
Sbjct: 300 VAVIGAGTMGGGIAMNFLNAGIAVKMLETKQEALDRGVATIQKNYEDRVKKGKLKEEKAA 359

Query: 63  VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISE 122
               +   T     +K +D VIEAV ED+ +K  +F+  +A   P A+LA+NTS+L +++
Sbjct: 360 QRMALLSTTLSYDDIKDADLVIEAVFEDMGVKEAVFKQLDAVMKPGAILASNTSTLDLNK 419

Query: 123 IASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVP 182
           IA   K PQ VVG+HFF+P  +M L+E+VRGKDT+ +V+ T  ++AK + K  ++     
Sbjct: 420 IAHFTKRPQDVVGLHFFSPANVMKLLEVVRGKDTAKDVLATAMDVAKKIKKIAVLSGVCD 479

Query: 183 GFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK 242
           GF  NR++ +      +L+++G    Q VD  AIE+ G+ MG F ++D  G DIG+S+ K
Sbjct: 480 GFIGNRMIDQYGRQAGFLLDEGCTPAQ-VD-RAIEKFGWAMGPFRMSDLAGNDIGWSIRK 537

Query: 243 AVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPS------PGKFVRPTLPSTSKKLG 296
              A         + + L  QG+ G K+G+G+Y Y        P K V   +    + LG
Sbjct: 538 RQYAENPTRRYSKTADLLCEQGRFGQKTGAGWYDYKPGKRDAIPNKDVEAMIAKHRESLG 597

Query: 297 ------------RYLISPAVNEVSYLLREGIVGK-DDAEKGCVLGLGLP---KGILSYAD 340
                       + L    VNE +++L EGI  K  D +   + G G P    G ++YAD
Sbjct: 598 IKPRKISDEEIVQRLNFALVNEAAHILEEGIASKASDIDMVYISGYGFPIFRGGPMNYAD 657

Query: 341 EIGIDVVVNTLEEMRQT--SGMDHYSPDPLLLSMVKEGK 377
           E+G+  VV  ++          + + P PLL  +  EGK
Sbjct: 658 ELGLFNVVQAMQRFATNPHDDAEFWKPAPLLAKLAAEGK 696



 Score = 99.4 bits (246), Expect = 5e-25
 Identities = 63/200 (31%), Positives = 97/200 (48%), Gaps = 10/200 (5%)

Query: 402 RVEPPLAWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVT 461
           +V   +A I LN P   N +  +  R +   +   +    V+ + ITG G+ FS GADV 
Sbjct: 6   QVHGDVAVITLNNPP-VNGMGLETRRALVAGIAQAQADAAVKAVVITGHGKAFSGGADVR 64

Query: 462 EFGSLTPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAE 521
           EFGS               V   ++   KPV+A ++ + +GGG+ELAL   +RV +    
Sbjct: 65  EFGS----PKAFQEPNLLSVISCVENCNKPVVAAMHTVVMGGGLELALGCHYRVCAPGTS 120

Query: 522 MGQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLG----IVEFLAEP 576
           +  PE+ LGLIPG GGTQRL R  G    + ++++G  +K++    L       +    P
Sbjct: 121 ISMPEVKLGLIPGAGGTQRLPRALGVEPAMNMIVSGEAIKSDMLSMLPGQKLFDQMAMSP 180

Query: 577 EELESEVRKLANAIAEKSPL 596
           + L  E    A  +A+  PL
Sbjct: 181 QSLMDEAIAYAREVADVRPL 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: 935
Number of extensions: 52
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: 699
Length adjustment: 39
Effective length of query: 612
Effective length of database: 660
Effective search space:   403920
Effective search space used:   403920
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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