GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Caldicellulosiruptor hydrothermalis 108

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate WP_013403450.1 CALHY_RS07950 methionine ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc02121
         (258 letters)



>NCBI__GCF_000166355.1:WP_013403450.1
          Length = 343

 Score =  186 bits (471), Expect = 7e-52
 Identities = 102/244 (41%), Positives = 148/244 (60%), Gaps = 7/244 (2%)

Query: 19  IEITNMNKWYG----DFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGK 74
           I I N+ K Y     D   L ++NL + +G+   + GPSG+GKST+IRCIN LE+   G 
Sbjct: 2   IRIKNLTKIYHSNGIDIKALDNVNLNIEKGDIFGIIGPSGAGKSTLIRCINMLEKPTHGS 61

Query: 75  IVVDGIELTN-DLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKEAEQV 133
           I +DG+E+T     ++ E+R++VG++FQHFNL    T+  N    P+ +  + KK  +  
Sbjct: 62  IEIDGVEMTKLSPTELKEMRKKVGIIFQHFNLLSSRTVKGNVAF-PLEIAGLDKKTIDNR 120

Query: 134 AMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVKEVL 193
               LE V +  +   YP QLSGGQ+QRV IAR+L   PK+LL DE TSALDPE    +L
Sbjct: 121 VKELLELVGLTNKTDSYPSQLSGGQKQRVGIARALANNPKVLLCDEATSALDPETTLSIL 180

Query: 194 DTMVGLAEE-GMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHERTKLF 252
           + +  +  E G+T++ VTHEM   +Q+ N+V  M++GQIVEQ    E F NP+ +  + F
Sbjct: 181 NLLKEINREFGITIVVVTHEMNVVKQICNKVAVMEKGQIVEQGLLTEIFANPKTKIAQNF 240

Query: 253 LSQI 256
           L  +
Sbjct: 241 LRSL 244


Lambda     K      H
   0.322    0.136    0.397 

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: 234
Number of extensions: 12
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: 258
Length of database: 343
Length adjustment: 26
Effective length of query: 232
Effective length of database: 317
Effective search space:    73544
Effective search space used:    73544
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