GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etoh-dh-nad in Pseudomonas fluorescens FW300-N2E3

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate AO353_07245 AO353_07245 alcohol dehydrogenase

Query= BRENDA::A4IP64
         (395 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_07245 AO353_07245 alcohol
           dehydrogenase
          Length = 382

 Score =  318 bits (814), Expect = 2e-91
 Identities = 176/373 (47%), Positives = 246/373 (65%), Gaps = 7/373 (1%)

Query: 15  GWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPL 74
           G GA++QL  E+ RL   + L++TD  LVK G V+   + L   G +  ++  V+P+P +
Sbjct: 15  GAGAIEQLAAELTRLDVDNPLIVTDAALVKSGTVELALAQLG--GRTYEIFDRVLPDPEI 72

Query: 75  ETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGL 134
              E  +   R+G  D +IG+GGGSA+D+AK  A  A + G++ D   L G   + +KG 
Sbjct: 73  AIVEDCMRVYREGGHDGLIGLGGGSAIDIAKSVAAYAGYHGALED---LFGIDQVPRKGP 129

Query: 135 PKILIPTTSGTGSEVTNISVLS--LETTKDVVTHDYLLADVAIVDPQLTVSVPPRVTAAT 192
           P I IPTT+GTGSEVTN+++LS  +   K  +  DYLL DVA+V PQ+T++ P  VTAA+
Sbjct: 130 PLIAIPTTAGTGSEVTNVAILSDRVAQLKKGIISDYLLPDVALVSPQMTLTCPRSVTAAS 189

Query: 193 GIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAG 252
           G+DAL HAVE+Y+S+NASP +D LA+ AI+LI ++L KA  N S+ QAR DMA  S +AG
Sbjct: 190 GVDALVHAVESYLSLNASPITDALAIGAIKLIIKALPKAYTNPSNLQAREDMATASLMAG 249

Query: 253 LAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADIFNALGGNS 312
           +AF NAGV  VHALAYPLGG+F++ HG SNA+LLPYVM + + +C +RM DI  ALG  +
Sbjct: 250 MAFGNAGVGAVHALAYPLGGRFNVTHGVSNALLLPYVMAWNKMACIERMQDIAEALGVKT 309

Query: 313 SFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLPL 372
           + LS  EA+ + VE + R  A V IP+ L   GIPE A+ ++  +A   +RL+  +P  L
Sbjct: 310 AQLSAEEAADKAVEAMARLCAAVEIPQGLHSLGIPEDAIPAMAVEAAGIERLMRNNPRKL 369

Query: 373 LEADIRAIYEAAF 385
             ADI  IY AA+
Sbjct: 370 STADIEKIYRAAY 382


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: 421
Number of extensions: 23
Number of successful extensions: 4
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: 382
Length adjustment: 30
Effective length of query: 365
Effective length of database: 352
Effective search space:   128480
Effective search space used:   128480
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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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