GapMind for catabolism of small carbon sources

 

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

Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate WP_084200485.1 C0029_RS02360 SDR family NAD(P)-dependent oxidoreductase

Query= BRENDA::Q99714
         (261 letters)



>NCBI__GCF_002869505.1:WP_084200485.1
          Length = 257

 Score =  240 bits (613), Expect = 2e-68
 Identities = 139/257 (54%), Positives = 167/257 (64%), Gaps = 6/257 (2%)

Query: 8   VKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLG-NNCVFAPADVT 66
           + G VA++TGGASGLG  T E  V +GA   + DL     +A    LG +N  F   +V 
Sbjct: 3   LNGKVAIVTGGASGLGQGTVEAYVAKGAKVAIFDLNAERAQAVVDNLGADNVAFWSVNVA 62

Query: 67  SEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTF 126
            E +V+TA+A    KFG + V  N AGI  A+KTY  KKG    +E +  V+ +NL GTF
Sbjct: 63  DENNVRTAIAEVVEKFGAIHVVNNFAGIGSAAKTYG-KKG-VFPIEQWDPVIAINLTGTF 120

Query: 127 NVIRLVAGEMGQNEP--DQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIAR 184
           NV R  A +M +NE   D GG RGVIINTASVA +EGQVGQ AYSA+KGG++GMT+P+AR
Sbjct: 121 NVSRYAAEQMSRNEQINDDGG-RGVIINTASVAGYEGQVGQVAYSATKGGVIGMTVPMAR 179

Query: 185 DLAPIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENP 244
           DLA  GIRV TI PGL  TPL  SLPE     L + V +P RLG PAE AHL   I EN 
Sbjct: 180 DLAGYGIRVNTIVPGLIHTPLFESLPEPAYKSLEASVCYPQRLGKPAEIAHLSVFIAEND 239

Query: 245 FLNGEVIRLDGAIRMQP 261
           +LN E IRLDGAIRMQP
Sbjct: 240 YLNAECIRLDGAIRMQP 256


Lambda     K      H
   0.318    0.135    0.385 

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: 211
Number of extensions: 12
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: 261
Length of database: 257
Length adjustment: 24
Effective length of query: 237
Effective length of database: 233
Effective search space:    55221
Effective search space used:    55221
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 (21.7 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