Alignments for a candidate for ech in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Klebsiella michiganensis M5al

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 BWI76_RS13125 BWI76_RS13125 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__Koxy:BWI76_RS13125
          Length = 473

 Score =  182 bits (461), Expect = 4e-50
 Identities = 122/364 (33%), Positives = 189/364 (51%), Gaps = 17/364 (4%)

Query: 3   VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLK-EGVE 61
           V VIGSG MG GIAE+AA AG+ V + DI+ E + +A++ I+  L+     G L  E  +
Sbjct: 8   VAVIGSGTMGAGIAEVAAAAGHPVLIFDIAPEAVVRAIDGIRQRLASRVSRGKLATEQAD 67

Query: 62  QVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPIS 121
            +LAR+ P  + +  L  +  +IEA  E LE+K+ +F    A  SPS +L +NTSS+ I+
Sbjct: 68  ALLARLVPAAELSN-LADAQLIIEAASERLEVKKALFEQLAAICSPSTLLVSNTSSISIT 126

Query: 122 EIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDV 181
            IA+ +K P+RV G+HFFNP  +M LVE+V G  TS EVV+   +      K+ +  +  
Sbjct: 127 AIAAGIKHPERVAGLHFFNPAPVMKLVEVVSGLATSTEVVEQLCQWVSDWGKQPVRCRST 186

Query: 182 PGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVW 241
           PGF VNRV           +E+ +A+ + +D++  +  GFPMG   L D  G D+ +   
Sbjct: 187 PGFIVNRVARPFYAEAWRALEEQVAAPEVIDAALRDGGGFPMGPLALTDLIGQDVNF--- 243

Query: 242 KAVTARGFKAF-------PCSSTEKLVSQGKLGVKSGSGYYQYPSPGKFVRPTLPSTSKK 294
            AVT   F A        P    ++L   G+LG KSG G Y++P+  +  R     ++++
Sbjct: 244 -AVTCSVFNACWQDRRYQPSLLQQELALAGRLGKKSGQGVYRWPAEAQPERALAAVSAER 302

Query: 295 LGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEM 354
             + +    V E+  +L     G    E    L L   + ++ Y    G  VV+ + E  
Sbjct: 303 AAKRIKRDVVTELDEILLLETTG----ETALALSLQHGRPVVVYDHCAGDTVVLASAETT 358

Query: 355 RQTS 358
            Q +
Sbjct: 359 SQAA 362



 Score = 41.6 bits (96), Expect = 8e-08
 Identities = 20/70 (28%), Positives = 38/70 (54%)

Query: 300 ISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQTSG 359
           ++  VNE    L++G+   +D +    LG+  P+G L++ + +G   V+  LE +++  G
Sbjct: 392 VAMLVNEALDALQKGVASAEDIDTAMRLGVNYPRGPLAWGESLGWGRVLRLLENLQRHYG 451

Query: 360 MDHYSPDPLL 369
            + Y P  LL
Sbjct: 452 EERYRPCSLL 461



 Score = 37.4 bits (85), Expect = 2e-06
 Identities = 33/133 (24%), Positives = 51/133 (38%), Gaps = 11/133 (8%)

Query: 302 PAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQTSGMD 361
           P   E    L E +   +  +     G G P G L+  D IG DV       +      D
Sbjct: 197 PFYAEAWRALEEQVAAPEVIDAALRDGGGFPMGPLALTDLIGQDVNFAVTCSVFNACWQD 256

Query: 362 H-YSPDPLLLSMVKEGKLGRKSGQGFHTYAHEEAKYSTIVVRVEPPLAWIVLNRPTRYNA 420
             Y P  L   +   G+LG+KSGQG + +  E           +P  A   ++       
Sbjct: 257 RRYQPSLLQQELALAGRLGKKSGQGVYRWPAE----------AQPERALAAVSAERAAKR 306

Query: 421 INGDMIREINQAL 433
           I  D++ E+++ L
Sbjct: 307 IKRDVVTELDEIL 319



 Score = 34.3 bits (77), Expect = 1e-05
 Identities = 16/77 (20%), Positives = 35/77 (45%)

Query: 148 VEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVPGFFVNRVLLRIMEAGCYLVEKGIAS 207
           V +   + TS           +   K+ + + D PG  V R +  ++      ++KG+AS
Sbjct: 350 VVLASAETTSQAATDKATFYFQQQGKKVLQIADYPGLLVWRTVAMLVNEALDALQKGVAS 409

Query: 208 IQEVDSSAIEELGFPMG 224
            +++D++    + +P G
Sbjct: 410 AEDIDTAMRLGVNYPRG 426


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: 582
Number of extensions: 26
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 4
Length of query: 651
Length of database: 473
Length adjustment: 36
Effective length of query: 615
Effective length of database: 437
Effective search space:   268755
Effective search space used:   268755
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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, or view the source code.

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