GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Lactobacillus silagei IWT126

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_089136416.1 CES79_RS04320 ABC transporter ATP-binding protein

Query= uniprot:A0A165KQ08
         (355 letters)



>NCBI__GCF_002217945.1:WP_089136416.1
          Length = 314

 Score =  168 bits (426), Expect = 2e-46
 Identities = 101/258 (39%), Positives = 147/258 (56%), Gaps = 9/258 (3%)

Query: 5   LDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGE 64
           +++  +NK +    +    L  + + +  GE  +LVGPSG GK+TLL  I  L  PT G+
Sbjct: 2   IELLNVNKEY----QEQHALDHLSLTINDGELFVLVGPSGSGKTTLLKTINRLVVPTSGQ 57

Query: 65  IRIGGKNV--VGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122
           ++I GK+V  V +    R I  V Q+ AL+P ++VA+N    L+  K P  ++ +RI E+
Sbjct: 58  VKIDGKDVADVDLQQLRRRIGYVLQTGALFPNMTVAENASVQLDNLKWPAEKKHERIAEL 117

Query: 123 AAMLQIS--HLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAE 180
              + +   H LDR PS+LSGG+ QRV + RALA +P L L DE  S LD   R +++  
Sbjct: 118 MTEVGLDPDHFLDRMPSELSGGEAQRVGIVRALAAKPGLVLMDESFSALDPVSRRQLQQI 177

Query: 181 IKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIG 240
           +  LH+    T V+VTHD  EA+ L  RIAV+  G +QQ+GTP EI   PAN +V++F  
Sbjct: 178 VINLHRDLDSTIVFVTHDMHEALRLADRIAVVYNGKLQQVGTPTEILTEPANAFVSSFFA 237

Query: 241 SPTM-NLLRGAVTGGQFG 257
                + L G V    FG
Sbjct: 238 DEQQTDQLLGQVLAAGFG 255


Lambda     K      H
   0.318    0.135    0.388 

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: 259
Number of extensions: 10
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: 355
Length of database: 314
Length adjustment: 28
Effective length of query: 327
Effective length of database: 286
Effective search space:    93522
Effective search space used:    93522
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: 49 (23.5 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