GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Azospirillum brasilense Sp245

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate AZOBR_RS13230 AZOBR_RS13230 alcohol dehydrogenase

Query= CharProtDB::CH_000596
         (353 letters)



>FitnessBrowser__azobra:AZOBR_RS13230
          Length = 340

 Score =  144 bits (362), Expect = 4e-39
 Identities = 98/273 (35%), Positives = 144/273 (52%), Gaps = 13/273 (4%)

Query: 7   QNMKAAVMHNTR-EIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVE-- 63
           + MKAAV+   +  + IE +PVP++   ++L+K+ A G+C +DLH       G++ V+  
Sbjct: 3   KTMKAAVVRQFKMPLSIEEVPVPEVGPGQILVKIEASGVCHTDLH----AADGDWPVKPN 58

Query: 64  KPFILGHECAGEIAAVGSSVDQFKVGDRVAVE-PGVTCGRCEACKEGRYNLCPDVQFLAT 122
            PFI GHE  G +AAVG+ V   K GDRV V      CG C  C  G   LC D+Q    
Sbjct: 59  PPFIPGHEGVGTVAAVGTGVTAVKEGDRVGVPWLHTACGHCRQCLAGWETLC-DLQQNTG 117

Query: 123 PPVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAAR-TKLQPGSTIAIMGM 181
             V+G F +Y     ++V  +PD L +E AA I    V ++   + T  +PG T+ I G+
Sbjct: 118 YSVNGGFAEYTLADPNYVGHLPDRLDWEMAAPILCAGVTVYKGLKETDTKPGDTVVISGI 177

Query: 182 GPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDRG 241
           G +G +AV  AKA G   +I  D+   +L  A+ MGA   IN +  D + E+K +    G
Sbjct: 178 GGLGHIAVQYAKAMGL-DVIAVDISDEKLALARAMGADAAINAKTTDPVAEVKALCG--G 234

Query: 242 VDVAWETAGNPAALQSALASVRRGGKLAIVGLP 274
                 TA +  A   AL  + + G +A+VGLP
Sbjct: 235 AQGVLVTAVSRHAFNQALGMLAKRGTMALVGLP 267


Lambda     K      H
   0.320    0.137    0.401 

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: 321
Number of extensions: 21
Number of successful extensions: 6
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: 353
Length of database: 340
Length adjustment: 29
Effective length of query: 324
Effective length of database: 311
Effective search space:   100764
Effective search space used:   100764
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: 49 (23.5 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