GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Azospirillum brasilense Sp245

Align furfuryl alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate AZOBR_RS13230 AZOBR_RS13230 alcohol dehydrogenase

Query= metacyc::MONOMER-17184
         (342 letters)



>FitnessBrowser__azobra:AZOBR_RS13230
          Length = 340

 Score =  467 bits (1202), Expect = e-136
 Identities = 230/338 (68%), Positives = 268/338 (79%)

Query: 1   MPAMMKAAVVRAFGAPLTIDEVPVPQPGPGQVQVKIEASGVCHTDLHAADGDWPVKPTLP 60
           M   MKAAVVR F  PL+I+EVPVP+ GPGQ+ VKIEASGVCHTDLHAADGDWPVKP  P
Sbjct: 1   MAKTMKAAVVRQFKMPLSIEEVPVPEVGPGQILVKIEASGVCHTDLHAADGDWPVKPNPP 60

Query: 61  FIPGHEGVGYVSAVGSGVSRVKEGDRVGVPWLYSACGYCEHCLQGWETLCEKQQNTGYSV 120
           FIPGHEGVG V+AVG+GV+ VKEGDRVGVPWL++ACG+C  CL GWETLC+ QQNTGYSV
Sbjct: 61  FIPGHEGVGTVAAVGTGVTAVKEGDRVGVPWLHTACGHCRQCLAGWETLCDLQQNTGYSV 120

Query: 121 NGGYGEYVVADPNYVGLLPDKVGFVEIAPILCAGVTVYKGLKVTDTRPGQWVVISGIGGL 180
           NGG+ EY +ADPNYVG LPD++ +   APILCAGVTVYKGLK TDT+PG  VVISGIGGL
Sbjct: 121 NGGFAEYTLADPNYVGHLPDRLDWEMAAPILCAGVTVYKGLKETDTKPGDTVVISGIGGL 180

Query: 181 GHVAVQYARAMGLRVAAVDIDDAKLNLARRLGAEVAVNARDTDPAAWLQKEIGGAHGVLV 240
           GH+AVQYA+AMGL V AVDI D KL LAR +GA+ A+NA+ TDP A ++   GGA GVLV
Sbjct: 181 GHIAVQYAKAMGLDVIAVDISDEKLALARAMGADAAINAKTTDPVAEVKALCGGAQGVLV 240

Query: 241 TAVSPKAFSQAIGMVRRGGTIALNGLPPGDFGTPIFDVVLKGITIRGSIVGTRSDLQESL 300
           TAVS  AF+QA+GM+ + GT+AL GLPPG F   IF  VL   TIRGSIVGTR DL E L
Sbjct: 241 TAVSRHAFNQALGMLAKRGTMALVGLPPGSFELDIFSTVLMRKTIRGSIVGTRLDLAECL 300

Query: 301 DFAAHGDVKATVSTAKLDDVNDVFGRLREGKVEGRVVL 338
            FA  G VK   S   LD++N+VF R+R  +++GRVV+
Sbjct: 301 QFAGDGKVKVHYSVEHLDNINNVFSRMRNNEIDGRVVM 338


Lambda     K      H
   0.319    0.139    0.427 

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: 400
Number of extensions: 15
Number of successful extensions: 1
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: 342
Length of database: 340
Length adjustment: 29
Effective length of query: 313
Effective length of database: 311
Effective search space:    97343
Effective search space used:    97343
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 (21.7 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