GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Williamsia sterculiae CPCC 203464

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_076479152.1 BW971_RS10155 crotonase/enoyl-CoA hydratase family protein

Query= CharProtDB::CH_091794
         (261 letters)



>NCBI__GCF_900156495.1:WP_076479152.1
          Length = 273

 Score =  117 bits (294), Expect = 2e-31
 Identities = 81/253 (32%), Positives = 131/253 (51%), Gaps = 14/253 (5%)

Query: 14  VAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVAGADISEMK- 72
           VA VT+  P   NA+  D  +E+  V  E++ D+EV AV+L G G K F  G D+S M  
Sbjct: 15  VAEVTLIGPGKGNAMGPDFWRELPEVFAELDADTEVRAVVLAGRG-KHFSFGLDLSAMAG 73

Query: 73  EMNTIEGRKFGILGNKVFRRLELLEK-----------PVIAAVNGFALGGGCEIAMSCDI 121
           E+  +            F R+ L  +           PV+A + G+ +GGG ++  + DI
Sbjct: 74  ELGPVLAGDALAKTRTEFHRMVLRMQGATTAVARSRTPVVAVIQGWCIGGGVDLIAAADI 133

Query: 122 RIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNK 181
           R AS++A F   E  +G+    G  QRL  ++G    ++L FTA++I AD ALRI LVN 
Sbjct: 134 RYASADATFSVREAKVGMVADMGSLQRLPAIIGDAHTRELAFTAKDIDADAALRINLVND 193

Query: 182 VVEPSE-LMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFSTE 240
           V+  ++  + TA+  A +I +N P+ V+  K  ++  +   +D  L + +        ++
Sbjct: 194 VLPDADAALATARATAAQIAANPPLVVQGVKDVLDWPLTGTVDDGLRYVAAWNAAFLPSK 253

Query: 241 DQKDAMTAFIEKR 253
           D  +A++A  EKR
Sbjct: 254 DIGEAISAIFEKR 266


Lambda     K      H
   0.317    0.134    0.365 

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: 141
Number of extensions: 7
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 261
Length of database: 273
Length adjustment: 25
Effective length of query: 236
Effective length of database: 248
Effective search space:    58528
Effective search space used:    58528
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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