GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lctC in Sinorhizobium meliloti 1021

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized)
to candidate SMc00728 SMc00728 electron transfer flavoprotein alpha-subunit alpha-ETF flavoprotein

Query= BRENDA::H6LBB1
         (418 letters)



>lcl|FitnessBrowser__Smeli:SMc00728 SMc00728 electron transfer
           flavoprotein alpha-subunit alpha-ETF flavoprotein
          Length = 309

 Score =  142 bits (357), Expect = 2e-38
 Identities = 103/324 (31%), Positives = 169/324 (52%), Gaps = 30/324 (9%)

Query: 74  ITVYVDHIEGQIHPVTFELIGKARELAAVIGHPVYALLMGTNITEKADELLKY-GVDKVF 132
           I +  DH    +   T     KA   AA IG  V+ L+ G N+   A++  K  GV KV 
Sbjct: 3   ILLLADHDNSHLSDQT----AKALTAAAKIGGDVHVLVAGQNVKGIAEQASKLSGVAKVL 58

Query: 133 VYDKPELKHFVIEPYANVLEDFIEKVKPSSILVGATNVGRSLAPRVAARYRTGLTADCTI 192
           V +   L + + EP A ++          +++  AT+VG+++ PRVAA           +
Sbjct: 59  VAEDASLANNLAEPLAALIVSLAGNY--DTVVAAATSVGKNVMPRVAA-----------L 105

Query: 193 LEMKENTDLVQI-------RPAFGGNIMAQIVTENTRPQFCTVRYKVFTAPERVNEPWGD 245
           L++ + ++++++       RP + GN +  + T   + +  TVR   F A +        
Sbjct: 106 LDVAQVSEIIEVVSADTYRRPIYAGNAIQTVQTSEPQ-KVITVRTASFAAAQEGGS--AP 162

Query: 246 VEMMDIEKAKLVSAIEVMEVIKKEKGIDLSEAETIVAVGRGV-KCEKDLDMIHEFAEKIG 304
           VE +       +SA  V + +      +L+ A+ I++ GR +   EK  ++I   A+K+G
Sbjct: 163 VETVAAAANPGLSA-HVSDALSSSDRPELTSAKIIISGGRALGSSEKFKEVILPVADKLG 221

Query: 305 ATVACTRPGIEAGWFDARLQIGLSGRTVKPKLIIALGISGAVQFAAGMQNSEYIIAINSD 364
           A V  +R  ++AG+     Q+G +G+ V P L IA GISGA+Q  AGM++S+ I+AIN D
Sbjct: 222 AAVGASRAAVDAGYAPNDWQVGQTGKVVAPDLYIACGISGAIQHLAGMKDSKVIVAINKD 281

Query: 365 PKAPIFNIAHCGMVGDLYEILPEL 388
            +APIF +A  G+V DL+E+LPEL
Sbjct: 282 EEAPIFQVADYGLVADLFEVLPEL 305


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: 268
Number of extensions: 16
Number of successful extensions: 2
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: 309
Length adjustment: 29
Effective length of query: 389
Effective length of database: 280
Effective search space:   108920
Effective search space used:   108920
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: 49 (23.5 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