GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SMc00728
          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:

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