GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Frischella perrara PEB0191

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_039106013.1 FPB0191_RS10720 sulfate/molybdate ABC transporter ATP-binding protein

Query= reanno::WCS417:GFF4321
         (386 letters)



>NCBI__GCF_000807275.1:WP_039106013.1
          Length = 359

 Score =  223 bits (569), Expect = 5e-63
 Identities = 113/238 (47%), Positives = 161/238 (67%), Gaps = 6/238 (2%)

Query: 4   LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63
           + L+N+NK++     + LKNI  SIK+GE + L+GPSGCGK+TL+  IAGLET + G I 
Sbjct: 3   ITLQNINKSFKNF--NALKNINFSIKQGELVALLGPSGCGKTTLLRIIAGLETASSGKIY 60

Query: 64  IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIR----KMPQADIDAEVARV 119
             D DV+ +S K RDI  VFQ+YAL+  M+V EN+ FGLK++    ++ +  I+  V ++
Sbjct: 61  FTDTDVTPLSAKQRDIGFVFQNYALFRHMNVAENVAFGLKMKPRSIRLSKTAINERVNQL 120

Query: 120 AKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMK 179
             L+Q+E+   R P QLSGGQ+QRVA+ RALA +P + L DEP S LDAK+R ++R  ++
Sbjct: 121 LGLVQLENFAKRYPDQLSGGQRQRVALARALASKPNVLLLDEPFSALDAKVRKDLRRWLR 180

Query: 180 LMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIG 237
             H  L  T+++VTHDQ EA+ + DK+ +M  G I+Q GTP E+Y  P   FVA F+G
Sbjct: 181 DFHHELNVTSIFVTHDQDEALEVADKIILMNQGQIEQIGTPTEVYKQPKTAFVAHFLG 238


Lambda     K      H
   0.318    0.135    0.382 

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: 340
Number of extensions: 12
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: 386
Length of database: 359
Length adjustment: 30
Effective length of query: 356
Effective length of database: 329
Effective search space:   117124
Effective search space used:   117124
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.

Links

Downloads

Related tools

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