GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Dyella japonica UNC79MFTsu3.2

Align histidine transport ATP-binding protein hisP (characterized)
to candidate N515DRAFT_2043 N515DRAFT_2043 putative ABC transport system ATP-binding protein

Query= CharProtDB::CH_003210
         (257 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2043
          Length = 230

 Score =  129 bits (325), Expect = 4e-35
 Identities = 91/233 (39%), Positives = 131/233 (56%), Gaps = 17/233 (7%)

Query: 6   LNVIDLHKRYGEH----EVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGS 61
           + V DL K Y       EVL  ++L    GD ++++G SGSGK+T L  I  L+ P+ GS
Sbjct: 7   IEVRDLSKVYERGKQKVEVLHHINLNIAEGDFLALMGPSGSGKTTLLNLIGGLDSPTGGS 66

Query: 62  IVVNGQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVL 121
           I V GQ I+       QL      + R     +  VFQ +NL   +T   NV E P+ + 
Sbjct: 67  IGVGGQRID-------QLGAGALAKWRA--ANVGFVFQFYNLMPMLTAQRNV-ELPLLLT 116

Query: 122 GLSKQEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTS 181
            LS  + R+ A   L  VG+DER+  K P  LSGGQQQRV+IARA+  +P +L+ DEPT 
Sbjct: 117 KLSAAQRRKNAAIALQLVGLDERSSHK-PSELSGGQQQRVAIARAIVSDPTLLVCDEPTG 175

Query: 182 ALDPELVGEVLRIMQQL-AEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEE 233
            LD +   +VL +++ L  E GKT+V+VTH+   A + + H + L +G + E+
Sbjct: 176 DLDRQSAEDVLGLLRTLNREHGKTIVMVTHDPKAAEY-ANHTLHLDKGTLVEQ 227


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: 148
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: 230
Length adjustment: 23
Effective length of query: 234
Effective length of database: 207
Effective search space:    48438
Effective search space used:    48438
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: 46 (22.3 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