Alignments for a candidate for ech in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Stenotrophomonas chelatiphaga DSM 21508

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_057507300.1 ABB28_RS03505 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_001431535.1:WP_057507300.1
          Length = 687

 Score =  162 bits (411), Expect = 4e-44
 Identities = 119/372 (31%), Positives = 178/372 (47%), Gaps = 17/372 (4%)

Query: 3   VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVEQ 62
           V V+G+GVMG  IA  +A  G  V + D     +  AM+R +    K     S +  V  
Sbjct: 314 VHVVGAGVMGGDIAAWSAYKGFNVTLQDREQRFIDPAMQRAQTLFEKKVRDESKRPAVA- 372

Query: 63  VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISE 122
             AR+  +   A A + +D VIEA+ E+ + KR +++  E      A+L TNTSS+P+ E
Sbjct: 373 --ARLQADLAGAGAAQ-ADLVIEAIIENPQAKRDLYQTLEPKMKADALLTTNTSSIPLIE 429

Query: 123 IASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVP 182
           +   ++ P +  G+H+FNP   MPLVEI+     + E  +  A   K++ K  + V   P
Sbjct: 430 LRDHIQRPAQFAGLHYFNPVAQMPLVEIIHHDGMAPETERRLAAFCKALGKFPVPVAGTP 489

Query: 183 GFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK 242
           GF VNRVL   M        +GI     +D +A+ + G PMG   L D  GLD+   V +
Sbjct: 490 GFLVNRVLFPYMLEAATAYAEGIPG-PVIDKAAV-KFGMPMGPIELLDTVGLDVAAGVGE 547

Query: 243 AVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGKFVRPTLPSTSKKLGRY---L 299
            +    F      +  + V  GK G K G G Y + + G+  +P +P   +  G     L
Sbjct: 548 ELAP--FLGLQIPAALQTVEPGKRGKKDGQGIYAWEN-GRAKKPEVPKGYQAPGDLEDRL 604

Query: 300 ISPAVNEVSYLLREGIVGKDD-AEKGCVLGLGLPK---GILSYADEIGIDVVVNTLEEMR 355
           I P +NE    L EG+V   D  + G + G G      G + Y    G D +V  L+ ++
Sbjct: 605 ILPLLNEAVACLHEGVVADADLLDAGVIFGTGFAPFRGGPVQYIRATGADALVERLKVLQ 664

Query: 356 QTSGMDHYSPDP 367
           Q  G D +SP P
Sbjct: 665 QRHG-DRFSPRP 675



 Score = 85.9 bits (211), Expect = 6e-21
 Identities = 57/174 (32%), Positives = 93/174 (53%), Gaps = 7/174 (4%)

Query: 410 IVLN---RPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSL 466
           +VLN   +    NA++ D++ E+   ++ +       V+  + +   F AGAD+ EF   
Sbjct: 23  VVLNLDRQDANVNAMSQDVLLELGDLIERIAIDPPKGVVIQSAKKAGFIAGADLKEFQEF 82

Query: 467 TPVKAMI-ASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASK--TAEMG 523
                +  A R+    + K+  L  P +A I+G  LGGG ELAL+  +RVAS   +  +G
Sbjct: 83  DRRGTVNDAIRRGQVTYQKLAELPCPTVAAIHGHCLGGGTELALACRYRVASNDSSTRIG 142

Query: 524 QPEINLGLIPGGGGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEP 576
            PE  LG+ PG GG+ RL +L G    ++++LTGR + A  A  +G+V+ +  P
Sbjct: 143 LPETQLGIFPGWGGSARLPQLVGAPAAMDMMLTGRTLSASAARNIGLVDKVVAP 196



 Score = 46.2 bits (108), Expect = 5e-09
 Identities = 36/115 (31%), Positives = 52/115 (45%), Gaps = 7/115 (6%)

Query: 281 GKFVRPTLPSTSKKLGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYAD 340
           GKF  P   +    + R L  P + E +    EGI G    +K  V   G+P G +   D
Sbjct: 479 GKFPVPVAGTPGFLVNRVLF-PYMLEAATAYAEGIPGPV-IDKAAVK-FGMPMGPIELLD 535

Query: 341 EIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGKLGRKSGQGFHTYAHEEAK 395
            +G+DV     EE+    G+      P  L  V+ GK G+K GQG + + +  AK
Sbjct: 536 TVGLDVAAGVGEELAPFLGLQI----PAALQTVEPGKRGKKDGQGIYAWENGRAK 586


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: 914
Number of extensions: 44
Number of successful extensions: 9
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: 687
Length adjustment: 39
Effective length of query: 612
Effective length of database: 648
Effective search space:   396576
Effective search space used:   396576
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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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