GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gntB in Desulfovibrio vulgaris Hildenborough

Align TRAP-type large permease component (characterized, see rationale)
to candidate 208332 DVU2823 TRAP dicarboxylate transporter family protein

Query= uniprot:Q930R2
         (425 letters)



>lcl|MicrobesOnline__882:208332 DVU2823 TRAP dicarboxylate
           transporter family protein
          Length = 591

 Score =  288 bits (738), Expect = 2e-82
 Identities = 160/410 (39%), Positives = 241/410 (58%), Gaps = 17/410 (4%)

Query: 14  MAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIPFFILAGELMNAGG 73
           +A+GVP+A  L    +  +   G    + IAQ      D+F ++AIPFFI AG  M AGG
Sbjct: 182 LAVGVPIAIGLGLAALATIIAAGTLPIEYIAQVAFTSIDSFPIMAIPFFIAAGVFMGAGG 241

Query: 74  LSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAAILIPMMAKAGYNV 133
           LSRR++  A   +G + GG+ +  I   +  A+ISGS  A  AA+ ++ IP M + GY+ 
Sbjct: 242 LSRRLLTLADEMLGSLHGGMALATIGTCMFFAAISGSGPATVAAIGSLTIPAMVERGYDK 301

Query: 134 PRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLIMGIALVAT----- 188
             SA ++AA G I  +IPPS  F+V+GV+A VSI +LF+ GIVPG++ G+AL+       
Sbjct: 302 YFSAAVVAAAGAIGVMIPPSNPFVVYGVSAQVSIGKLFLGGIVPGVLTGLALMVYSYWYS 361

Query: 189 ----WLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEAAVVA 244
               W   VR  +++   R        A   A WAL +PVI+LGGI  G++TPTEAA +A
Sbjct: 362 KKRGWKGEVRVRNLRTFTR--------ALWDAKWALMVPVIVLGGIYGGIMTPTEAAALA 413

Query: 245 AVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSEITGF 304
           A Y LFVG  I+REL    L   I++AA T+AV++ L+  A +   ++T   +P+ I   
Sbjct: 414 AFYGLFVGCFIHRELNCGSLYDCIVEAAGTSAVVIVLMAMATIFGNIMTIEEVPTAIATA 473

Query: 305 ISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVLFIMN 364
           +  L +    ++ +I ++++V+GT ++    I+ILTP+L+PI+ + G+DPV+FGV+ ++N
Sbjct: 474 MLNLTENKIAILMLINVLLIVIGTFMEALAAIVILTPILLPIVLKVGVDPVHFGVIMVVN 533

Query: 365 TCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFP 414
             IG + PPVGV L V SGV    +  +   V P +   I VL L+   P
Sbjct: 534 LAIGFVPPPVGVNLFVASGVAHAKIEHLSKVVMPLIAIMIGVLLLITYVP 583


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: 571
Number of extensions: 27
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: 425
Length of database: 591
Length adjustment: 34
Effective length of query: 391
Effective length of database: 557
Effective search space:   217787
Effective search space used:   217787
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 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