GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ech in Acidovorax sp. GW101-3H11

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 Ac3H11_2523 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

Query= BRENDA::A4YDS4
         (651 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2523 Enoyl-CoA hydratase
           (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA
           isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase
           (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC
           5.1.2.3)
          Length = 699

 Score =  190 bits (483), Expect = 2e-52
 Identities = 128/399 (32%), Positives = 205/399 (51%), Gaps = 26/399 (6%)

Query: 3   VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVEQ 62
           V VIG+G MG GI+     AG  V + ++  E L + +  IK +     + G LK+    
Sbjct: 300 VGVIGAGTMGGGISMNFLNAGIPVKILEMKQEALDRGVATIKKNYEAQVKKGKLKQDKYD 359

Query: 63  VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISE 122
               +   T      K  D +IEAV E++ +K  +F+  +A A P A+LA+NTS+L + +
Sbjct: 360 QRMALLSTTLSYDDFKDCDLIIEAVFEEMGVKEAVFKQLDAVAKPGAILASNTSTLDVDK 419

Query: 123 IASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVP 182
           IA+  K PQ VVGMHFF+P  +M L+E+VRGK+T+ +V+ T   + K + K ++V     
Sbjct: 420 IAAFTKRPQDVVGMHFFSPANVMKLLEVVRGKETAKDVLATVMAIGKKIKKTSVVSGVCD 479

Query: 183 GFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK 242
           GF  NR++ +      +L+++G  + Q+VD  A+E+ GF MG F + D  G DIG+++ K
Sbjct: 480 GFIGNRMIEQYSRQAGFLLDEG-CTPQQVD-KAVEKFGFAMGPFRMGDLAGNDIGWAIRK 537

Query: 243 AVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPS------PGKFVRPTLPSTSKKLG 296
             +          + +KL   G+ G K+G+G+Y Y +      P   V   +    K+LG
Sbjct: 538 RRSVERADMKYSRTADKLCELGRFGQKTGAGWYDYQAGKRDAIPSDLVNKMIEDHRKELG 597

Query: 297 ------------RYLISPAVNEVSYLLREGIVGKD-DAEKGCVLGLGLP---KGILSYAD 340
                       + L+   VNE +++L +GI  K  D +   + G G P    G + YA 
Sbjct: 598 ITPRKISDEEIVQRLVFALVNEGAHILEDGIASKSGDIDMVYLTGYGFPIHRGGPMHYAS 657

Query: 341 EIGIDVVVNTLEEMRQTSGMD--HYSPDPLLLSMVKEGK 377
           E+G+  VV  ++   +    D   + P PLL  +  EGK
Sbjct: 658 EVGLFNVVQAMDRFARNPLDDAAFWKPAPLLAKLAAEGK 696



 Score =  102 bits (253), Expect = 8e-26
 Identities = 62/163 (38%), Positives = 89/163 (54%), Gaps = 15/163 (9%)

Query: 442 VRVIAITGQGRVFSAGADVTEFGSLTPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLAL 501
           V+ I ITG G  FS GAD+ EFG+       +       V   I+   KPV+A ++ +A+
Sbjct: 45  VKSIVITGAGGAFSGGADIKEFGT----DKSLQEPNLLSVIAAIENSAKPVVAAMHSVAM 100

Query: 502 GGGMELALSADFRVASKTAEMGQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVK 560
           GGG+ELAL   +R+A+    +  PE+ LGLIPG GGTQRL R+ G    L L+++G  VK
Sbjct: 101 GGGLELALGCHYRIAAPGCSIALPEVKLGLIPGAGGTQRLPRVIGVEAALNLIVSGEPVK 160

Query: 561 AEEAYRLGIV-------EFLAEPEELESEVRKLANAIAEKSPL 596
           +E    +G V       +  A  E L +E    A ++A+  PL
Sbjct: 161 SE---MIGAVPGQKLFDKMAASAESLAAEALAFAQSVADARPL 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: 933
Number of extensions: 59
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 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 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