GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5503 in Williamsia sterculiae CPCC 203464

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_076482473.1 BW971_RS17350 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q9HT70
         (335 letters)



>NCBI__GCF_900156495.1:WP_076482473.1
          Length = 250

 Score =  178 bits (452), Expect = 1e-49
 Identities = 100/234 (42%), Positives = 139/234 (59%), Gaps = 10/234 (4%)

Query: 18  IPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVE---------GED 68
           +  L+   L ++ G++  LIG SG+GKST LR +N LE  + GR+ V+         G  
Sbjct: 14  LQVLKGISLEVERGEVTCLIGPSGSGKSTFLRCVNHLESVTAGRLYVDDDLIGYREKGGK 73

Query: 69  VTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLAR 128
           +  L A+     R+ +GM+FQHFNL   +T  DNI        G  RA    R  +LL +
Sbjct: 74  LYELSAKDAAAQRRDIGMVFQHFNLFPHRTALDNIIEAPIQVKGVVRARAVERGKDLLDQ 133

Query: 129 VGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEIN 188
           VGL+D A  YPAQLSGGQ+QRV IARALA  P ++L DE TSALDP+    VL ++  + 
Sbjct: 134 VGLADKASAYPAQLSGGQQQRVAIARALAMDPKLMLFDEPTSALDPELVGDVLAVMRNLA 193

Query: 189 RELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFV 242
           ++  +T+V++THEM   R V DQ+  MD G +VE+GD  +V   PQH  T+ F+
Sbjct: 194 KD-GMTMVVVTHEMGFAREVADQLVFMDAGKVVEKGDPREVLNSPQHERTQSFL 246


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: 230
Number of extensions: 8
Number of successful extensions: 3
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: 250
Length adjustment: 26
Effective length of query: 309
Effective length of database: 224
Effective search space:    69216
Effective search space used:    69216
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: 48 (23.1 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