GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Pseudomonas stutzeri RCH2

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate GFF3713 Psest_3782 Alcohol dehydrogenase, class IV

Query= BRENDA::A4IP64
         (395 letters)



>FitnessBrowser__psRCH2:GFF3713
          Length = 388

 Score =  232 bits (591), Expect = 2e-65
 Identities = 141/367 (38%), Positives = 209/367 (56%), Gaps = 7/367 (1%)

Query: 5   RIVFPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHV 64
           RIV P L  VG GA  QL   +K LG    L++TD M+V++G V ++   L + G +   
Sbjct: 4   RIVLPRLMEVGAGASQQLARVLKELGCNRPLIVTDRMMVELGYVARIAGQLGEAGIASQC 63

Query: 65  YTDVVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLT 124
           + D +PEP   +    V   R G FD ++ +GGGS +D AK   +L    G + DY    
Sbjct: 64  FADTLPEPTAASIRAGVEMVRQGDFDSIVALGGGSPIDSAKAIGILGKFGGEMRDY---R 120

Query: 125 GTRTLEKKGLPKILIPTTSGTGSEVTNISVLSLETTKDVVTHDYL--LADVAIVDPQLTV 182
             R + + GLP I IPTT+GTGSE T  ++++ ET+ + +    L  +   A++D +LT+
Sbjct: 121 FPRDVSEAGLPLIAIPTTAGTGSEATRFTIITDETSDEKMLCAGLGFMPIAALIDYELTL 180

Query: 183 SVPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARI 242
           S+PPRVTA TGIDALTHA+EAYVS  AS  SD  A+ A+RL++ +LR A     ++ AR 
Sbjct: 181 SLPPRVTADTGIDALTHAIEAYVSRKASLYSDAQALEAMRLLAPNLRAAFHEPGNRAARE 240

Query: 243 DMANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMA 302
            M  G+ LAG+AF NA VA VH ++ P+G  FH+ HG SNA+LLP +  +   +  +R A
Sbjct: 241 AMMLGATLAGIAFSNASVALVHGMSRPIGAFFHVPHGLSNAMLLPAITAFSIPAAPERYA 300

Query: 303 DIFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQK 362
           D   A+G  +   S   A+ + + EL     ++ +P     FGI       L ++ + ++
Sbjct: 301 DCARAMGVAAQTDSVGVANDKLLAELRAINQELQVPSP-EQFGISRERFFEL-RETMARQ 358

Query: 363 RLLARSP 369
            L + SP
Sbjct: 359 ALASGSP 365


Lambda     K      H
   0.318    0.135    0.381 

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: 378
Number of extensions: 19
Number of successful extensions: 3
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: 395
Length of database: 388
Length adjustment: 31
Effective length of query: 364
Effective length of database: 357
Effective search space:   129948
Effective search space used:   129948
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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