GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xyrA in Pandoraea thiooxydans ATSB16

Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate WP_047215429.1 PATSB16_RS18075 aldo/keto reductase

Query= BRENDA::F2YCN5
         (340 letters)



>NCBI__GCF_001931675.1:WP_047215429.1
          Length = 327

 Score =  428 bits (1101), Expect = e-125
 Identities = 210/323 (65%), Positives = 251/323 (77%), Gaps = 3/323 (0%)

Query: 16  IKGIDKSATRVALGTWAIGGWMWGGTDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEV 75
           I GI    +R+ LGTWAIGGWMWGG DD ASI TI  AID GIN+IDTAP YG GHAEEV
Sbjct: 8   IDGIATPVSRIGLGTWAIGGWMWGGADDTASIATIRNAIDQGINLIDTAPVYGFGHAEEV 67

Query: 76  VGKAIKGQRDNLIIATKVGLDWTLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQV 135
           VGKA++G+R+  +IATKV L+W    D  ++RNS+ +RI+ EIEDSLRRL TD IDLYQV
Sbjct: 68  VGKALEGRREQAVIATKVALEWG---DDGIKRNSTPARIRTEIEDSLRRLRTDRIDLYQV 124

Query: 136 HWPDPLVPIEETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYAELAVSQSPYNLFERE 195
           HWPDP VP EETA  LE LR+EGKI +IGVSN+S +QMD F + A LA  Q PYNLFER 
Sbjct: 125 HWPDPRVPFEETAAELEKLRQEGKILAIGVSNFSPEQMDVFGRAARLAAVQPPYNLFERA 184

Query: 196 IDKDILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKTDPKFQKPRFEHYLAA 255
           I+ D+LPYAK + L VL YGALCRGLLSGRM+A   F GDDLR  DPKFQ PRF  YLAA
Sbjct: 185 IEADVLPYAKSHGLTVLAYGALCRGLLSGRMSASTRFDGDDLRNHDPKFQPPRFAQYLAA 244

Query: 256 VEELKKLAKEHYNKSVLALAIRWMLEQGPTLALWGACKPEQIDGIDEVFGWQISDEDLKQ 315
           V  L +L+ + + KSVLALAIRW+L+QGPT+ALWGA +P+Q+ GID+ FGW++S  DL  
Sbjct: 245 VGALAQLSHDRHGKSVLALAIRWILDQGPTIALWGARRPDQLRGIDDAFGWRLSPGDLAD 304

Query: 316 IDAILAKNIPNPIGAEFMAPPPR 338
           IDA+LA++I +P+G EFMAPP R
Sbjct: 305 IDALLARHITSPVGPEFMAPPLR 327


Lambda     K      H
   0.317    0.136    0.407 

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: 406
Number of extensions: 13
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: 340
Length of database: 327
Length adjustment: 28
Effective length of query: 312
Effective length of database: 299
Effective search space:    93288
Effective search space used:    93288
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: 49 (23.5 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