GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Pantoea rwandensis LMG 26275

Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_084931116.1 HA51_RS00225 SDR family oxidoreductase

Query= uniprot:B2T9V3
         (247 letters)



>NCBI__GCF_002095475.1:WP_084931116.1
          Length = 258

 Score =  132 bits (332), Expect = 7e-36
 Identities = 88/255 (34%), Positives = 137/255 (53%), Gaps = 14/255 (5%)

Query: 4   RLAGKTALITAAGQGIGLATAELFAREGARVIATDIR--IDGLA-----GKPVEARKLDV 56
           R  GK  LIT A  G+G   A  +AREGA +   D     D +A     G+   A K DV
Sbjct: 2   RYQGKNVLITGAAAGLGQTIATSYAREGASIAIIDFADASDTVAKVQASGQQAVAFKADV 61

Query: 57  RDDAAIKAL---AAEI--GAVDVLFNCAGFVHAGNILECSE-EDWDFAFDLNVKAMYRMI 110
           RD  A++A    AA +  G +DVL N AGF    N++E      W    D+N+     + 
Sbjct: 62  RDQDAVQAAVNQAANVFAGRIDVLINNAGFNGHYNLVENMPLAQWRETLDINLTGTLLVT 121

Query: 111 RAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCN 170
           +A +P M  +GGG+I  ++++  + +G+P R  Y  SK A++GL +++A + +   +R N
Sbjct: 122 QAVIPFMKAQGGGAI-GITASNVARRGLPYRADYVCSKWALLGLNQTLALELVDHHIRVN 180

Query: 171 AICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDE 230
           A+CPG +    +E  +V QA+A+G +L  ++ A+    PM R    EE+ A  ++L SD 
Sbjct: 181 AVCPGPIEGDRIEDVMVRQAEAEGKSLKEMRKAWEEAAPMKRFVTAEEVTAAMMFLTSDA 240

Query: 231 SSFTTGHAHVIDGGW 245
           +S  TG A  + GG+
Sbjct: 241 ASAMTGQALNVTGGF 255


Lambda     K      H
   0.320    0.133    0.381 

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: 137
Number of extensions: 10
Number of successful extensions: 4
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: 247
Length of database: 258
Length adjustment: 24
Effective length of query: 223
Effective length of database: 234
Effective search space:    52182
Effective search space used:    52182
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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