GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctC in Azospirillum brasilense Sp245

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate AZOBR_RS05475 AZOBR_RS05475 protein fixB

Query= BRENDA::H6LBB1
         (418 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS05475 AZOBR_RS05475 protein fixB
          Length = 359

 Score =  231 bits (590), Expect = 2e-65
 Identities = 126/324 (38%), Positives = 193/324 (59%), Gaps = 6/324 (1%)

Query: 71  YRGITVYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTNITEK---ADELLKYG 127
           Y+GI V V+   G +H V++EL+G+AR+LA  +G  V A+++G +  E      +   YG
Sbjct: 21  YKGIWVIVEQERGSVHSVSWELVGEARKLADKLGVEVGAVVLGADSPELNAICGDAFTYG 80

Query: 128 VDKVFVYDKPELKHFVIEPYANVLEDFIEKVKPSSILVGATNVGRSLAPRVAARYRTGLT 187
            D V+    P L  +  +PY  V+ D +   KP  +L+GAT +GR LA  +A    TGLT
Sbjct: 81  ADVVYKVTDPVLADYRTDPYTRVMTDVVNTYKPEIVLLGATTLGRDLAGAIATTLATGLT 140

Query: 188 ADCTILEM-KENTDLVQIRPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGDV 246
           ADCT L++  +N  L   RP FGG ++  I T   RPQ  TVR +V + P+R +   G V
Sbjct: 141 ADCTELDIYMDNRSLAATRPTFGGTLLCTIQTLAYRPQMATVRPRVMSMPDRDDSRTGRV 200

Query: 247 EMM--DIEKAKLVSAIEVMEVIKKEKGIDLSEAETIVAVGRGVKCEKDLDMIHEFAEKIG 304
             +  ++ +  +++ +      +++    L+ A+ IVA G+G+   ++L ++ + A+ +G
Sbjct: 201 VEVFPNLRETDVITKVLSFIADREQTEAQLAFADIIVAAGKGLGKPENLKLVFDLAKVLG 260

Query: 305 ATVACTRPGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSD 364
             V  TRP ++AGW     Q+G +G+TV+PKL IA GISGA+Q   GM+ S+ I+AIN+D
Sbjct: 261 GEVGVTRPLVQAGWTGFDRQVGQTGKTVRPKLYIAAGISGAIQHRVGMEKSDLILAINTD 320

Query: 365 PKAPIFNIAHCGMVGDLYEILPEL 388
           P APIF+ AH G+VGD   ILP L
Sbjct: 321 PNAPIFDFAHLGLVGDALTILPAL 344


Lambda     K      H
   0.319    0.137    0.395 

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: 401
Number of extensions: 18
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: 418
Length of database: 359
Length adjustment: 30
Effective length of query: 388
Effective length of database: 329
Effective search space:   127652
Effective search space used:   127652
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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