GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctD in Azospirillum brasilense Sp245

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate AZOBR_RS12240 AZOBR_RS12240 2-hydroxy-acid oxidase

Query= BRENDA::H6LBS1
         (466 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS12240 AZOBR_RS12240
           2-hydroxy-acid oxidase
          Length = 467

 Score =  229 bits (585), Expect = 1e-64
 Identities = 156/460 (33%), Positives = 235/460 (51%), Gaps = 16/460 (3%)

Query: 12  AAIKELIPAERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPV 71
           A  K L+  +R      + E    DE    +  P+ +   TSTEEVS I+    +H +P+
Sbjct: 19  AEFKALL-GDRFTTAAAVREHHGKDESYHPNFPPDGVAFATSTEEVSAIVTLCAKHKLPI 77

Query: 72  VVRGSGTGLVGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEENDL 131
           +  G+GT L G    L GG+ ++ + M  +L +  E+L VTV+ GV   +L++ + +  L
Sbjct: 78  IPFGTGTSLEGGVAALAGGVCIDVSNMKEVLRVSPEDLDVTVQAGVTRKQLNEHLRDTGL 137

Query: 132 FYPPDPGEKSATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNSS 191
           F+P DPG   A++ G  ST A G  AV+YG  R+ V GLTVVLA+G II+ GG+  K+++
Sbjct: 138 FFPIDPGA-DASLGGMASTRASGTNAVRYGTMRENVLGLTVVLADGRIIKTGGRARKSAA 196

Query: 192 GYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAIPT 251
           GY L  L +G+EGTL +IT+  L+L  +P+   S + PF +I  A   V + I+S     
Sbjct: 197 GYDLTRLFVGAEGTLGIITEVTLRLYGIPEAISSAVCPFNDIRGAVDTVIQTIQSGIPVA 256

Query: 252 AIEFMERQTILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGAKD 311
            IE ++   +    D + K        A  L      T   V+ + E VA +    G  +
Sbjct: 257 RIELLDEVQM----DAVNKYSKLDYKVAPTLFFEFHGTAAGVKEQAEMVAAIAAEFGGSE 312

Query: 312 VYIVDTVERKDSVWSAR--GAFLEAIKASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMD 369
                  E +  +W AR  G +        ++    DV VP +R+A+ I  T     E  
Sbjct: 313 FTWATRPEDRSKLWQARHDGYYAALALRPGSKGWPTDVCVPISRLADCILETKKDIAESS 372

Query: 370 VRIPSFGHAGDGNLHIYVCRDELCQADWEAKLAEAM---DRMYAKALTFEGLVSGEHGIG 426
           +  P  GH GDGN H+    D     D   +LAEA    DRM  +AL   G  +GEHGIG
Sbjct: 373 MLAPLVGHVGDGNFHLVYVID----PDKPEELAEAKRLNDRMVDRALAMGGTCTGEHGIG 428

Query: 427 YAKRKYLLNDFGTEHLALMAGIKQTFDPKNLLNPKKVCQM 466
           Y K ++L  + G +  A+M  +K+ FDP+N +NP KV ++
Sbjct: 429 YGKMEFLEKEAG-DAFAVMGELKRAFDPENRMNPGKVVRI 467


Lambda     K      H
   0.318    0.136    0.388 

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: 525
Number of extensions: 27
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: 466
Length of database: 467
Length adjustment: 33
Effective length of query: 433
Effective length of database: 434
Effective search space:   187922
Effective search space used:   187922
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: 51 (24.3 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