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 8501197 DvMF_1931 TRAP dicarboxylate transporter, DctM subunit (RefSeq)

Query= uniprot:Q930R2
         (425 letters)



>FitnessBrowser__Miya:8501197
          Length = 640

 Score =  298 bits (764), Expect = 2e-85
 Identities = 155/404 (38%), Positives = 247/404 (61%), Gaps = 1/404 (0%)

Query: 14  MAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIPFFILAGELMNAGG 73
           + +GVP+AFSL    +  +   G    + +AQ      D+F +LAIPFFI AG  M AGG
Sbjct: 232 LLVGVPIAFSLGLATIATVLGAGTLPLEYLAQIAFVSIDSFPILAIPFFIAAGVFMGAGG 291

Query: 74  LSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAAILIPMMAKAGYNV 133
           LSRR++      VG + GG+ +  I+  +  A+ISGS  A  AA+ +I IP M + GY+ 
Sbjct: 292 LSRRLLALGDELVGALPGGMALATIVTCMFFAAISGSGPATVAAIGSITIPAMVERGYDK 351

Query: 134 PRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLIMGIALVAT-WLLV 192
             +A ++A+ G I  +IPPS  F+V+GVAA  S+ +LF+AGIVPG++ G+AL+A  + + 
Sbjct: 352 FFAAAVVASAGCIGVMIPPSNPFVVYGVAAQASVGKLFLAGIVPGVLCGLALMAVAYYIS 411

Query: 193 VRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEAAVVAAVYALFVG 252
           ++K           +  + A   A WAL +PVI+LGGI  G++TPTEAA V+A+Y + VG
Sbjct: 412 LKKGWRGEARHRDFRSVMQAMWEAKWALLVPVIVLGGIYGGIMTPTEAAAVSALYGMIVG 471

Query: 253 MVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSEITGFISPLIDRP 312
           + IYRE+  R +   ++++A+T++VI+ L+  A +   ++T   +P  I   I  +    
Sbjct: 472 LFIYREITWRRMWDCMVESAQTSSVIIVLMAMATLFGNIMTIEQVPDHIAAMILGVTSNK 531

Query: 313 TLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVLFIMNTCIGLLTP 372
             ++ +I + +L VGT ++    I+I+TP+L+P++ Q G+DP++FGV+ ++N  IG +TP
Sbjct: 532 IAILLLINVFLLWVGTFMEALAAIVIITPILLPLVTQVGVDPIHFGVIMVVNLAIGFITP 591

Query: 373 PVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDI 416
           PVGV L V S + +V +G V+    PFL+  I +L  +   P I
Sbjct: 592 PVGVNLFVASSISKVSIGDVVRAAWPFLLVMIALLMAITYIPAI 635


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: 679
Number of extensions: 35
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 425
Length of database: 640
Length adjustment: 35
Effective length of query: 390
Effective length of database: 605
Effective search space:   235950
Effective search space used:   235950
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: 52 (24.6 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