Alignments for a candidate for hisP in Hydrogenovibrio marinus DSM 11271

GapMind for catabolism of small carbon sources

Alignments for a candidate for hisP in Hydrogenovibrio marinus DSM 11271

Align Histidine transport ATP-binding protein HisP (characterized)
to candidate WP_035629258.1 P166_RS0103830 ABC transporter ATP-binding protein

Query= SwissProt::P02915
         (258 letters)



>NCBI__GCF_000711315.1:WP_035629258.1
          Length = 550

 Score =  128 bits (322), Expect = 2e-34
 Identities = 84/262 (32%), Positives = 140/262 (53%), Gaps = 30/262 (11%)

Query: 10  IDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKS----TFLRCINFLEKPSEGAIIV 65
           ++L K +    ++  VS + +AG++ +++G SGSGKS      +R +    + S GAI +
Sbjct: 15  VELEKNH--RPLISNVSFEIKAGEIFALVGESGSGKSLTSLAIMRLLPEALQVSSGAISL 72

Query: 66  NGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQV---- 121
           N Q         G   + +    ++   ++ M+FQ       MT L  VM+   QV    
Sbjct: 73  NHQ---------GLFSLPEYQMQKVRGRQVAMIFQE-----PMTSLNPVMKVGDQVAEVL 118

Query: 122 ---LGLSKHDARERALKYLAKVGID--ERAQGKYPVHLSGGQQQRVSIARALAMEPDVLL 176
              LG+++  ARE+ +    +VGI   E     YP  LSGGQ+QRV IA ALA EPD+L+
Sbjct: 119 RVHLGMNRKTAREKVVSLFDEVGIPNPEERYDWYPHQLSGGQKQRVMIAMALACEPDLLI 178

Query: 177 FDEPTSALDPELVGEVLRIMQQLAEE-GKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEG 235
            DEPT+ALD  +  +VL +++Q+ ++ G  ++ +TH+MG    ++  V  +  G+I E+ 
Sbjct: 179 ADEPTTALDVTIQAQVLNLLKQIRDDRGLAILFITHDMGVVNEIADRVAVMKDGEIVEQA 238

Query: 236 DPEQVFGNPQSPRLQQFLKGSL 257
           +    F +PQ P  Q+ L  ++
Sbjct: 239 ETGHFFTDPQHPYTQKLLSDAI 260



 Score =  117 bits (293), Expect = 5e-31
 Identities = 81/256 (31%), Positives = 140/256 (54%), Gaps = 16/256 (6%)

Query: 12  LHKRYGGH-EVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGAIIVNGQNI 70
           + +R  GH + + GV+L    G  ++++G SGSGKST  + I  L   + G        +
Sbjct: 293 IFQRTVGHVKAVDGVNLTIPKGQTLALVGESGSGKSTIGQAILKLVDATAG-------QV 345

Query: 71  NLVRDKDGQ-LKVADKNQ--LRLLRTRLTMVFQH--FNLWSHMTVLENVMEA--PIQVLG 123
           N   D+  Q + + D ++  ++  R ++ ++FQ     L   MT+ E + E    +QV  
Sbjct: 346 NFTNDQAAQAINLVDLSEKAMKPFRKKVQVIFQDPFSALNPRMTINEIIREGMNSLQVGP 405

Query: 124 LSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSA 183
            S+ +  +R    L +VG+    + +YP   SGGQ+QR+ IARALA+EP++++ DEPTSA
Sbjct: 406 KSRVEQDKRIESLLEQVGLLPEHKYRYPHEFSGGQRQRIGIARALAVEPELIICDEPTSA 465

Query: 184 LDPELVGEVLRIMQQLAEEGK-TMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFG 242
           LD  +  +VL +++ L +  + + + +TH++     ++ HV  +  GKI E+G  E+V  
Sbjct: 466 LDVSVRAQVLALLKDLQKTYQMSYLFITHDLSIVPSIAHHVAVMQAGKIVEQGLVEEVMQ 525

Query: 243 NPQSPRLQQFLKGSLK 258
           NPQ    Q+ L  + K
Sbjct: 526 NPQHDYTQRLLASAPK 541


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: 333
Number of extensions: 16
Number of successful extensions: 6
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: 550
Length adjustment: 30
Effective length of query: 228
Effective length of database: 520
Effective search space:   118560
Effective search space used:   118560
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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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