Alignments for a candidate for bztB in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for bztB in Desulfovibrio vulgaris Hildenborough

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate 206177 DVU0751 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family

Query= CharProtDB::CH_011913
         (426 letters)



>MicrobesOnline__882:206177
          Length = 596

 Score = 98.6 bits (244), Expect = 5e-25
 Identities = 57/140 (40%), Positives = 86/140 (61%), Gaps = 5/140 (3%)

Query: 284 FTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVI 343
           FTG F+    F    I L++YT+AF+AE++RAG+Q+I +G  EAAY+ GL   + +  +I
Sbjct: 133 FTGNFE----FWCATIGLSVYTSAFMAEVIRAGLQSIPKGLLEAAYSSGLNYVQVLRTII 188

Query: 344 LPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDLRGTLGGITLNQTGRELECMLLMMLIY 403
           LP A R I+PPL S+FLN  KNSSLA+ V   +L      +  + T +  E      ++Y
Sbjct: 189 LPMAFRAIIPPLGSEFLNNMKNSSLAMVVGVAELTWQSQQVE-SLTFKGFEATSAATVLY 247

Query: 404 LTISLTISSLMNLYNKSIKL 423
           L++SL IS ++N  N  ++L
Sbjct: 248 LSLSLLISFILNGVNGKMRL 267



 Score = 85.5 bits (210), Expect = 4e-21
 Identities = 44/91 (48%), Positives = 63/91 (69%)

Query: 294 FTALLIALTLYTAAFIAEIVRAGIQAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVP 353
           F +  IALTL+T A++AEIVRAGIQ I  GQ EAAY+ GL   +TM  +ILPQAL+ ++P
Sbjct: 460 FWSATIALTLFTGAYLAEIVRAGIQNIPAGQVEAAYSTGLTFVQTMRRIILPQALKQMIP 519

Query: 354 PLISQFLNLTKNSSLAIAVSYMDLRGTLGGI 384
            ++ QF+ + K++SLA  +  ++L     GI
Sbjct: 520 AIVGQFIAIFKDTSLAFVLGVLELTFVAQGI 550



 Score = 42.0 bits (97), Expect = 5e-08
 Identities = 33/105 (31%), Positives = 49/105 (46%), Gaps = 18/105 (17%)

Query: 57  DFNFSFLWTRAGYDLAQTLIPYSNDDTHFRAL----IEGLLNTLLVSVLGCILATILGTI 112
           DF + F W           I ++ + T+   L    ++GL  T+ +S++   LA  LGT+
Sbjct: 32  DFGYQFQWD----------ILFTRNTTYGTHLGLEILKGLGVTVRISLISSALALGLGTV 81

Query: 113 IGVLRLSQNWLVARIMTVYVETFRNIPLLL----WILLMGTILAE 153
           +G+ RLS    +    T  VE FRN PLL+    W      IL E
Sbjct: 82  LGIARLSLFAPLRLTATAVVEFFRNTPLLVQLFFWYFAFPAILPE 126



 Score = 37.7 bits (86), Expect = 1e-06
 Identities = 28/101 (27%), Positives = 47/101 (46%), Gaps = 7/101 (6%)

Query: 60  FSFLWTRAGYDLAQTLI---PYSNDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVL 116
           ++F W     +L   LI   P    D  F  L  GL  +LL++V+   ++  +G ++G+ 
Sbjct: 356 YNFNWGVIADNLRTLLIWHFPNGQSDELFMGL-GGLAYSLLMAVIAISVSFFIGLVVGIG 414

Query: 117 RLSQNWLVARIMTVYVETFRNIPLLL---WILLMGTILAET 154
           R S N +      +Y+E  R  PL++   WI     +L  T
Sbjct: 415 RTSDNRICRIPCLLYIELIRGNPLIIVIFWIYFFIPVLFNT 455


Lambda     K      H
   0.326    0.139    0.419 

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: 530
Number of extensions: 25
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 4
Length of query: 426
Length of database: 596
Length adjustment: 34
Effective length of query: 392
Effective length of database: 562
Effective search space:   220304
Effective search space used:   220304
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources