GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Halioglobus japonicus S1-36

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_102106187.1 C0029_RS04910 crotonase/enoyl-CoA hydratase family protein

Query= CharProtDB::CH_091794
         (261 letters)



>NCBI__GCF_002869505.1:WP_102106187.1
          Length = 269

 Score =  146 bits (368), Expect = 5e-40
 Identities = 92/261 (35%), Positives = 136/261 (52%), Gaps = 11/261 (4%)

Query: 5   NVILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVA 64
           N I+E+EG V +VT+NRP+A NA +   L  M      ++ D  +   ILT  G+ +F A
Sbjct: 7   NCIVEQEGNVLIVTLNRPEAKNAFSPQMLLGMYKAWRLLDEDDSLRCAILTANGD-TFCA 65

Query: 65  GADISE--------MKEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIA 116
           G D+           +E  T+ G    +    + R      KP+I AV G+AL GG EI 
Sbjct: 66  GMDLKAGADGDHGATEEFMTLMGEVPNVHWQALLRD-NRPNKPIILAVEGYALAGGTEIL 124

Query: 117 MSCDIRIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRI 176
              DIR+ + +A FG  EV  G+ P  G T RL R +   +A +++   +++ A +AL I
Sbjct: 125 QGTDIRVGAEDAVFGVTEVARGLYPMSGSTVRLRRQIPYCLAAEILLCGEHVSAQQALDI 184

Query: 177 GLVNKVVEPSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQC-DIDTALAFESEAFGE 235
           GL+NK+V     ++ AKE A KI +N P+AVK   Q++    +C   D A+       G 
Sbjct: 185 GLINKIVPKGTTLDAAKEYAAKICANGPLAVKAVVQSLREHQECMSEDDAMVASDALAGP 244

Query: 236 CFSTEDQKDAMTAFIEKRKIE 256
            F++ D K+ M AF EKR  E
Sbjct: 245 VFASNDAKEGMRAFKEKRPAE 265


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: 168
Number of extensions: 8
Number of successful extensions: 2
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: 269
Length adjustment: 25
Effective length of query: 236
Effective length of database: 244
Effective search space:    57584
Effective search space used:    57584
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.

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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