GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdaD in Azospirillum brasilense Sp245

Align Probable 2-keto-3-deoxyxylonate dehydratase; KDXD; EC 4.2.1.141 (characterized)
to candidate AZOBR_RS15905 AZOBR_RS15905 2-hydroxyhepta-2 4-diene-1 7-dioate isomerase

Query= SwissProt::D4GP28
         (289 letters)



>FitnessBrowser__azobra:AZOBR_RS15905
          Length = 283

 Score = 78.6 bits (192), Expect = 2e-19
 Identities = 71/215 (33%), Positives = 105/215 (48%), Gaps = 32/215 (14%)

Query: 90  ISEQAREEESSMPDMYFDVYDADRPEVFFKATPSRTVEPGDAIGV-RGDSEWDVPEPELG 148
           ++ +A   ES +P+          P +F KAT S    P D + + RG ++ D  E ELG
Sbjct: 78  LNYRAHAAESGLPE-------PAEPVLFMKATTS-ICGPNDPVQMPRGATKLDW-EVELG 128

Query: 149 IVLRR-----------GEIVGYTVGNDVSSRSIEGENPLYLPQAKVYDRCCSIGPCVVTP 197
           IV+ R             I GY V NDVS R+ + E+     + K  D  C IGP +VT 
Sbjct: 129 IVIGRTARYVEQADAFDHIAGYCVLNDVSERAFQTESTGQWVKGKSADSFCPIGPWMVTR 188

Query: 198 EDVEDPHELEMSMTIERDGEVIYDDATNTSEMVRSCDELVSYFTRHNTVPELAVILTGT- 256
           ++V DP  L   + +E DG+ + D  + T++M+    E+VSY +R  T+    VI TGT 
Sbjct: 189 DEVPDPQALR--LWLEVDGQPMQD--STTADMIFGVAEIVSYISRFMTLLPGDVIATGTP 244

Query: 257 -----SLVPEQPFDLQEGDHVDITIEGIGTLSNSV 286
                   P  P+ LQ G  + + +EG+G    SV
Sbjct: 245 QGVALGRGPNHPW-LQPGQTMRLGVEGLGEQRQSV 278


Lambda     K      H
   0.314    0.132    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: 184
Number of extensions: 7
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: 289
Length of database: 283
Length adjustment: 26
Effective length of query: 263
Effective length of database: 257
Effective search space:    67591
Effective search space used:    67591
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: 42 (22.0 bits)
S2: 47 (22.7 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