GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS12240
          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:

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