GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntB in Desulfovibrio vulgaris Miyazaki F

Align TRAP-type large permease component (characterized, see rationale)
to candidate 8501407 DvMF_2137 TRAP dicarboxylate transporter, DctM subunit (RefSeq)

Query= uniprot:Q930R2
         (425 letters)



>FitnessBrowser__Miya:8501407
          Length = 427

 Score =  319 bits (818), Expect = 9e-92
 Identities = 173/409 (42%), Positives = 249/409 (60%), Gaps = 5/409 (1%)

Query: 15  AIGVPVAFSLMFCGVVLMWYMGM-----FNTQIIAQNMIAGADTFTLLAIPFFILAGELM 69
           A+  PVA +L       +   G+         +  Q + AGAD+F LLA+P F+LAGELM
Sbjct: 15  ALNAPVAVALGGAAFAAVLAKGLTMPVGLEPMLAVQRLYAGADSFPLLAVPLFMLAGELM 74

Query: 70  NAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAAILIPMMAKA 129
           +AGG+SRRI+  A A VGH+ GGL  V++++A+  A +SGSAAADTAA+ +ILIP M + 
Sbjct: 75  SAGGISRRIVALADALVGHLPGGLAAVSVVSAMFFAGVSGSAAADTAAVGSILIPAMIRR 134

Query: 130 GYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLIMGIALVATW 189
           GY  P +  + AAGG I  +IPPS+  IVFG     SI +LF  G++PGL+MG +LVA  
Sbjct: 135 GYPAPLAGAVQAAGGCIGVIIPPSIPMIVFGALTGASIGRLFAGGVLPGLLMGASLVALC 194

Query: 190 LLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEAAVVAAVYAL 249
           ++  R+    P  R   +    A     WALG P IILG I  GV T TE+A +A  YAL
Sbjct: 195 VVEARRTGRVPERRFDARALWPAIRSGAWALGAPAIILGTIIGGVATATESAAMAVAYAL 254

Query: 250 FVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSEITGFISPLI 309
            VG+  +REL+ RDLP + L A  T+AV+M ++ AA +  W++    +P  I  ++  L 
Sbjct: 255 PVGLYAHRELRWRDLPRLALCAGVTSAVVMLIIAAASLFGWVMALERLPQAIAAWMLSLS 314

Query: 310 DRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVLFIMNTCIGL 369
               +L+ ++ L++LVVG  L+ T  IL+  PVL+P++   GID V+ GV+ ++N  IG+
Sbjct: 315 GDRIVLLLLVNLLLLVVGAFLETTAAILLFVPVLVPLLPALGIDLVHLGVIVVVNLAIGM 374

Query: 370 LTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDIVI 418
           LTPP+GV L V   + R+PL  +   + P LV  I+ L L+  FP +V+
Sbjct: 375 LTPPLGVCLVVSCSIARIPLSAISRAIVPMLVVLIVDLLLVTFFPPLVL 423


Lambda     K      H
   0.331    0.145    0.430 

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: 526
Number of extensions: 20
Number of successful extensions: 1
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: 425
Length of database: 427
Length adjustment: 32
Effective length of query: 393
Effective length of database: 395
Effective search space:   155235
Effective search space used:   155235
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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