GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt1d in Azospirillum brasilense Sp245

Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate AZOBR_RS13230 AZOBR_RS13230 alcohol dehydrogenase

Query= BRENDA::Q38707
         (365 letters)



>FitnessBrowser__azobra:AZOBR_RS13230
          Length = 340

 Score =  169 bits (427), Expect = 1e-46
 Identities = 103/320 (32%), Positives = 157/320 (49%), Gaps = 13/320 (4%)

Query: 36  GEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYP-IVPGHEIVGVVTEVGSKVEKVKVGDNV 94
           G   + +K+   GVCH+D H    +W     P  +PGHE VG V  VG+ V  VK GD V
Sbjct: 28  GPGQILVKIEASGVCHTDLHAADGDWPVKPNPPFIPGHEGVGTVAAVGTGVTAVKEGDRV 87

Query: 95  GIGCLVGSCRSCESCCDNRESHCENTIDTYGSIYFDGTMTHGGYSDTMVADEHFILRWPK 154
           G+  L  +C  C  C    E+ C+   +T       G   +GG+++  +AD +++   P 
Sbjct: 88  GVPWLHTACGHCRQCLAGWETLCDLQQNT-------GYSVNGGFAEYTLADPNYVGHLPD 140

Query: 155 NLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVGLGGLGHVAVKMAKAFGAQVTVID 214
            L  +  AP+LCAG+T Y  LK     KPG  + + G+GGLGH+AV+ AKA G  V  +D
Sbjct: 141 RLDWEMAAPILCAGVTVYKGLKETDT-KPGDTVVISGIGGLGHIAVQYAKAMGLDVIAVD 199

Query: 215 ISESKRKEALEKLGADSFLLNSDQE---QMKGARSSLDGIIDTVPVNHPLAPLFDLLKPN 271
           IS+ K   A   +GAD+ +     +   ++K       G++ T    H       +L   
Sbjct: 200 ISDEKLALA-RAMGADAAINAKTTDPVAEVKALCGGAQGVLVTAVSRHAFNQALGMLAKR 258

Query: 272 GKLVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKETQEMLDFAAKHNITADVEVIPMD 331
           G + +VG P   FEL +FS +  RK + G+I G   +  E L FA    +     V  +D
Sbjct: 259 GTMALVGLPPGSFELDIFSTVLMRKTIRGSIVGTRLDLAECLQFAGDGKVKVHYSVEHLD 318

Query: 332 YVNTAMERLVKSDVRYRFVI 351
            +N    R+  +++  R V+
Sbjct: 319 NINNVFSRMRNNEIDGRVVM 338


Lambda     K      H
   0.319    0.137    0.415 

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: 258
Number of extensions: 11
Number of successful extensions: 5
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: 365
Length of database: 340
Length adjustment: 29
Effective length of query: 336
Effective length of database: 311
Effective search space:   104496
Effective search space used:   104496
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