GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5503 in Halococcus hamelinensis 100A6

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_007693030.1 C447_RS08815 ATP-binding cassette domain-containing protein

Query= TCDB::Q9HT70
         (335 letters)



>NCBI__GCF_000336675.1:WP_007693030.1
          Length = 437

 Score =  166 bits (419), Expect = 1e-45
 Identities = 100/245 (40%), Positives = 141/245 (57%), Gaps = 5/245 (2%)

Query: 12  RVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTA 71
           R  GR + A+     ++  G+  GL+G SG GKST    + R EEP+ G I  +G D+ A
Sbjct: 25  REVGR-VRAVDGIDFDLDRGETLGLVGESGCGKSTAATTLLRFEEPTEGEIEFDGTDLLA 83

Query: 72  LDAEGLRRFRQRVGMIFQHFNLLSSK--TVADNIAMPLRLAGGFSRAEVDARVSELLARV 129
            D + L+RFR+R  M+FQ  N       T+ +++A PLR+ G   R    A V   L RV
Sbjct: 84  CDKDELKRFRRRAQMVFQDPNSSFDPRMTIGESVAEPLRVHG-LPRERRRAVVRNTLERV 142

Query: 130 GL-SDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEIN 188
           GL +  A +YP + SGGQKQR+ +ARAL   P +++ DE  SALD    A +L L+ +I 
Sbjct: 143 GLDATAADRYPHEFSGGQKQRIALARALVLNPDLIVADEPVSALDVSLQAEILTLIDDIQ 202

Query: 189 RELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFVFEAERV 248
           +E  L I+ I+H+M VI++VC++VAVM  G IVE G    VF  PQHP T+  +      
Sbjct: 203 QEFGLGILFISHDMSVIQQVCNRVAVMYLGEIVEIGSTDAVFSDPQHPYTQALLASIPNP 262

Query: 249 DEDER 253
           D  +R
Sbjct: 263 DPRKR 267


Lambda     K      H
   0.322    0.138    0.393 

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: 359
Number of extensions: 20
Number of successful extensions: 2
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: 335
Length of database: 437
Length adjustment: 30
Effective length of query: 305
Effective length of database: 407
Effective search space:   124135
Effective search space used:   124135
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 (21.9 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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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