GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Stutzerimonas stutzeri A1501

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA

Query= TCDB::P73721
         (252 letters)



>NCBI__GCF_000013785.1:WP_011911265.1
          Length = 279

 Score =  240 bits (613), Expect = 2e-68
 Identities = 127/259 (49%), Positives = 176/259 (67%), Gaps = 9/259 (3%)

Query: 3   SPTAPLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISG 62
           +P  P++ F  + K +G L VL G+  ++   + ++IIGPSG GKST LR L  LE I  
Sbjct: 20  APAQPMVRFASVTKRYGELTVLEGLDLDVQEGEKVAIIGPSGSGKSTLLRVLMTLEGIDD 79

Query: 63  GRLEVAGVDLSG--------AKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRK 114
           G +EV G  L+            + +HLR++R +VGMVFQ FNLFPH+  LQN++ AP +
Sbjct: 80  GLIEVDGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQSFNLFPHMNALQNVMEAPVQ 139

Query: 115 VLRIPMAEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPT 174
           VL +   EA++RA   L  VGL  K +++P QLSGGQ+QRVAIAR L M+P+++LFDE T
Sbjct: 140 VLGLSKREARERAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMRPKVMLFDEVT 199

Query: 175 SALDPELVGEVLNVMKQLAE-EGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEV 233
           SALDPEL GEVL+V+++L E   +TM +VTH+M FARE ++RV FF+QG I E+G P+ +
Sbjct: 200 SALDPELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGRIHEQGSPDAL 259

Query: 234 FRNPKSDRLRAFLSRIQSS 252
           F NP+ DR R FLS +  +
Sbjct: 260 FNNPQEDRTREFLSAVNEA 278


Lambda     K      H
   0.321    0.139    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: 199
Number of extensions: 7
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: 252
Length of database: 279
Length adjustment: 25
Effective length of query: 227
Effective length of database: 254
Effective search space:    57658
Effective search space used:    57658
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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