Alignments for a candidate for hisP in Sulfurivirga caldicuralii DSM 17737

GapMind for catabolism of small carbon sources

Alignments for a candidate for hisP in Sulfurivirga caldicuralii DSM 17737

Align Histidine transport ATP-binding protein HisP (characterized)
to candidate WP_074201299.1 BUQ81_RS05125 dipeptide ABC transporter ATP-binding protein

Query= SwissProt::P02915
         (258 letters)



>NCBI__GCF_900141795.1:WP_074201299.1
          Length = 545

 Score =  137 bits (344), Expect = 6e-37
 Identities = 88/242 (36%), Positives = 132/242 (54%), Gaps = 18/242 (7%)

Query: 24  GVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNINLVRDKDGQLKVA 83
           GV L  R G+ ++++G SGSGKST    +  L + +EG I+          D+   L   
Sbjct: 305 GVDLTIRPGETLALVGESGSGKSTLGMALLRLNELTEGQILF---------DEQVDLATL 355

Query: 84  DKNQLRLLRTRLTMVFQH----FNLWSHMTVLENVMEAPI--QVLGLSKHDARERALKYL 137
           ++  LR  R  + ++FQ     FN    MTV E++ E  I  +V    K   RER  + L
Sbjct: 356 NERALRPWRRHIQVIFQDPFAAFN--PRMTVGESIREGMITLKVGPQDKASQRERVAELL 413

Query: 138 AKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELVGEVLRIMQ 197
            KVG+      +YP   SGGQ+QR+ IARALA+EP +++ DEPTSALD  +  +++ ++ 
Sbjct: 414 QKVGLQPEHMDRYPHEFSGGQRQRLGIARALAVEPRLIICDEPTSALDVTVRAQIIDLLN 473

Query: 198 QLAEE-GKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQSPRLQQFLKGS 256
            L EE G + + +TH++     ++  V  + QGKI EEG  EQ+   PQ P  QQ L+ +
Sbjct: 474 TLQEEQGVSYLFITHDLSILPRIAHRVAVMQQGKIVEEGRVEQILRVPQHPYTQQLLEAA 533

Query: 257 LK 258
            K
Sbjct: 534 PK 535



 Score =  131 bits (329), Expect = 3e-35
 Identities = 88/249 (35%), Positives = 132/249 (53%), Gaps = 18/249 (7%)

Query: 18  GHEVLKGVSLQARAGDVISIIGSSGSGKS-TFLRCINFLEKP---SEGAIIVNGQNINLV 73
           G  +LKG+  + R G+V +++G SGSGKS T L  +  L +      G I +    +   
Sbjct: 23  GTPILKGIDFELRRGEVFALVGESGSGKSMTALAIMRLLPEGLRYDRGCIYLQDTEL--- 79

Query: 74  RDKDGQLKVADKNQLRLLRTRLTMVFQH--FNLWSHMTVLENVMEAPIQVLGLSKHDARE 131
                 L + +    R+   R+ M+FQ     L   MT+ E + EA    LGL     RE
Sbjct: 80  ------LSLPEAAMQRIRGRRIAMIFQEPMSALNPVMTIGEQIGEALKLHLGLRGRKQRE 133

Query: 132 RALKYLAKVGIDERAQGK--YPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSALDPELV 189
           R ++ L +VGI E       YP  LSGGQ+QRV IA ALA EPDVL+ DEPT+ALD  + 
Sbjct: 134 RVIQLLQEVGIPEPETRLDWYPHQLSGGQRQRVMIAMALACEPDVLIADEPTTALDVTIQ 193

Query: 190 GEVLRIMQQL-AEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFGNPQSPR 248
            ++L +++ L  + G  ++ +TH+MG    ++  V  ++ G+I E+ D      +P+ P 
Sbjct: 194 AQILDLLKSLQRKRGLAVLFITHDMGVVAEIADRVAVMYHGEIVEQADTRHFLIDPEHPY 253

Query: 249 LQQFLKGSL 257
            QQ LK +L
Sbjct: 254 TQQLLKNAL 262


Lambda     K      H
   0.319    0.136    0.383 

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: 357
Number of extensions: 18
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 258
Length of database: 545
Length adjustment: 30
Effective length of query: 228
Effective length of database: 515
Effective search space:   117420
Effective search space used:   117420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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