GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt1d in Herbaspirillum seropedicae SmR1

Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate HSERO_RS04830 HSERO_RS04830 alcohol dehydrogenase

Query= BRENDA::Q38707
         (365 letters)



>FitnessBrowser__HerbieS:HSERO_RS04830
          Length = 341

 Score =  162 bits (409), Expect = 2e-44
 Identities = 103/310 (33%), Positives = 154/310 (49%), Gaps = 13/310 (4%)

Query: 48  GVCHSDHHMIHNNWGFT-TYPIVPGHEIVGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSC 106
           GVCH+D H  H +W    T P +PGHE  G V  VG+ V+ VK GD VG+  L  +C  C
Sbjct: 40  GVCHTDLHAAHGDWPVKPTPPFIPGHEGTGYVAAVGAGVKHVKEGDRVGVPWLHTACGCC 99

Query: 107 ESCCDNRESHCENTIDTYGSIYFDGTMTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLC 166
             C    E+ C    +T       G   +G +++  +AD  F+   P NL     AP+LC
Sbjct: 100 SPCRTGWETLCAEQQNT-------GYSVNGSFAEYGLADPKFVGHLPDNLDFGPAAPVLC 152

Query: 167 AGITTYSPLKYYGLDKPGTKIGVVGLGGLGHVAVKMAKAFGAQVTVIDISESKRKEALEK 226
           AG+T Y  LK   + +PG  + + G+GGLGH+AV+ AKA G  V   DI E K   A +K
Sbjct: 153 AGVTVYKGLKETEV-RPGEWVVISGIGGLGHMAVQYAKAMGMHVVAADIHEDKLALA-KK 210

Query: 227 LGADSFLLNSDQE---QMKGARSSLDGIIDTVPVNHPLAPLFDLLKPNGKLVMVGAPEKP 283
           LGAD  +   +     +++       G + T      +   F  L+  G + +VG P   
Sbjct: 211 LGADLTVDGRNHNAVAEVQRIIGGAHGALVTAVSPKAMEQAFGFLRARGTMALVGLPPGD 270

Query: 284 FELPVFSLLKGRKLLGGTINGGIKETQEMLDFAAKHNITADVEVIPMDYVNTAMERLVKS 343
             LPVF+ +  R  + G+I G  ++ +E L FAA+  + A      +D +N    R+ + 
Sbjct: 271 ISLPVFNTVLKRITVRGSIVGTRQDLEESLVFAAEGKVAAHFTWDKLDNINAIFARMEEG 330

Query: 344 DVRYRFVIDI 353
            +  R V+D+
Sbjct: 331 KIDGRIVLDL 340


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: 284
Number of extensions: 17
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: 341
Length adjustment: 29
Effective length of query: 336
Effective length of database: 312
Effective search space:   104832
Effective search space used:   104832
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