GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Phaeacidiphilus oryzae TH49

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein

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



>NCBI__GCF_000744815.1:WP_037572389.1
          Length = 386

 Score =  224 bits (571), Expect = 3e-63
 Identities = 132/356 (37%), Positives = 201/356 (56%), Gaps = 15/356 (4%)

Query: 4   LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63
           L L  + K +G+     +  ++L+I +G F  L+G SGCGK+T +  I+GLE  T G I 
Sbjct: 19  LRLTGLTKKFGSFT--AVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIH 76

Query: 64  IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123
           +GDQDV+   P  R +  VFQ+YAL+P + + EN+ FGL+ R +    +   V  +  L+
Sbjct: 77  LGDQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGI--RSVKKPVEDMLDLV 134

Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
           ++ HL  RKP QLSGGQQQR+A+ RAL  +P++ L DEPL  LD KLR +M+ E+K +  
Sbjct: 135 ELGHLARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQL 194

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243
            +  T V+VTHDQ EAMT+ D +AVM  G I+Q G+P E+Y NP   FVA+F+G    N 
Sbjct: 195 EVGLTFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQ--SNL 252

Query: 244 VPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGD---S 300
           +   ++   G +V +   G++   LAL           VILG+RPE++ +A  E +    
Sbjct: 253 IAGTVESVSGDVVQVAAHGRS---LALPAARCRTTSGPVILGVRPEKVRIAKTEAEVPSG 309

Query: 301 ASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQV---GETLTLQFDPSK 353
           A+ +  +V      G  T   V+L   +       +   ++   G  + + +DPS+
Sbjct: 310 ANHLTGKVTDASFIGVSTQYLVELPSGEELAVFEQNTGQEIQRPGAEVVVHWDPSQ 365


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: 356
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 386
Length of database: 386
Length adjustment: 30
Effective length of query: 356
Effective length of database: 356
Effective search space:   126736
Effective search space used:   126736
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: 50 (23.9 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