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:

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:

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:

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:

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