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:

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