GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Flavobacterium glycines Gm-149

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate WP_066328438.1 BLR17_RS00855 iron-containing alcohol dehydrogenase

Query= BRENDA::A4IP64
         (395 letters)



>NCBI__GCF_900100165.1:WP_066328438.1
          Length = 380

 Score =  211 bits (536), Expect = 4e-59
 Identities = 146/389 (37%), Positives = 218/389 (56%), Gaps = 27/389 (6%)

Query: 5   RIVFPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHV 64
           R+VF      G G++ + V +    G K + +I    L    LV  +   L++ G +V V
Sbjct: 11  RVVF------GEGSMQRFVDDFVASGLKRMFLIGISELANT-LVPYIEK-LKENGVAVFV 62

Query: 65  YTDVVPEPPL----ETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADY 120
              +  EP      E  EKA+AF  D     V+GVGGGS LD+AKL A    +  S+ + 
Sbjct: 63  DESIKGEPTFDDFNEVLEKAIAFNADS----VVGVGGGSVLDVAKLVAAQLKNTQSLDE- 117

Query: 121 LNLTGTRTLEKKGLPKILIPTTSGTGSEVTNISVLSLETTKDV-VTHDYLLADVAIVDPQ 179
             + G   L+++      IPTTSGTGSEV+  ++      + V V   YL+ D A +DP 
Sbjct: 118 --IKGIGNLKERQTYVACIPTTSGTGSEVSPNAIFVNNLGEKVGVISPYLVPDAAYIDPV 175

Query: 180 LTVSVPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQ 239
           LTV +P  VTAATGIDALTH +EAY +  A P  D  A+  +RLI++ L++A  +G+D +
Sbjct: 176 LTVLLPKSVTAATGIDALTHCLEAYTNKFAHPFVDLYALEGVRLIAKYLKRACDDGTDIE 235

Query: 240 ARIDMANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGY-IRQSCT 298
           AR  +A GS   G+       A VHAL+YPLG ++HI HG SNA+LLPYVM Y I +  +
Sbjct: 236 ARTQVALGSMYGGMCLGPVNTAAVHALSYPLGVEYHIPHGLSNALLLPYVMEYNIEEDAS 295

Query: 299 K--RMADIFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTK 356
           K  R+A++  A   N+S  + +E     V+ +++ +AD G+P +L   G+ E ++  L +
Sbjct: 296 KYERIAEVLGAEKKNTSRETALEG----VKIMKQLIADCGLPTSLAHAGVKEESITKLAE 351

Query: 357 DAVQQKRLLARSPLPLLEADIRAIYEAAF 385
            A++ +RLL  +   +   D  AIY++AF
Sbjct: 352 GAIKVQRLLKNNIREIAVEDAVAIYQSAF 380


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: 333
Number of extensions: 14
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: 380
Length adjustment: 30
Effective length of query: 365
Effective length of database: 350
Effective search space:   127750
Effective search space used:   127750
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 24 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