GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2523
          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:

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