GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hisP in Bacteroides thetaiotaomicron VPI-5482

Align histidine transport ATP-binding protein hisP (characterized)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)

Query= CharProtDB::CH_003210
         (257 letters)



>lcl|FitnessBrowser__Btheta:351279 BT1751 Glycine betaine transport
           ATP-binding protein (NCBI ptt file)
          Length = 408

 Score =  149 bits (375), Expect = 1e-40
 Identities = 89/248 (35%), Positives = 143/248 (57%), Gaps = 18/248 (7%)

Query: 10  DLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVVNGQTI 69
           ++ K  G    +K  +L  N G++  I+G SGSGKST LRCIN L +P+ G +++NG  I
Sbjct: 32  EILKATGCTVAVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTDI 91

Query: 70  NLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKQEAR 129
                     KV+DK  L++ R  L MVFQ+F L  H +VL N+    +++ G+ K E  
Sbjct: 92  ---------AKVSDKELLQIRRKELAMVFQNFGLLPHRSVLHNIAFG-LELQGVKKGERE 141

Query: 130 ERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSALDP---- 185
           ++A++ +  VG+ +  + +    LSGG QQRV +ARALA  PEVLL DE  SALDP    
Sbjct: 142 QKAMESMQLVGL-KGYENQMVSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRV 200

Query: 186 ELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNPQS 245
           ++  E+L +  ++    KT+V +TH++  A  +   +  +  G+I + G  E++   P +
Sbjct: 201 QMQDELLTLQSKMK---KTIVFITHDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPAN 257

Query: 246 PRLQRFLK 253
             ++RF++
Sbjct: 258 AYVERFVE 265


Lambda     K      H
   0.318    0.134    0.375 

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: 243
Number of extensions: 11
Number of successful extensions: 4
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: 257
Length of database: 408
Length adjustment: 28
Effective length of query: 229
Effective length of database: 380
Effective search space:    87020
Effective search space used:    87020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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