GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Phaeacidiphilus oryzae TH49

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

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>NCBI__GCF_000744815.1:WP_037572389.1
          Length = 386

 Score =  207 bits (528), Expect = 3e-58
 Identities = 119/301 (39%), Positives = 177/301 (58%), Gaps = 21/301 (6%)

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

Query: 64  VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123
           + D D++   P  R +  VFQ+YAL+P + + +N+AFGL+ R + +  + + V  +  L+
Sbjct: 77  LGDQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGIRS--VKKPVEDMLDLV 134

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

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

Query: 244 IPLRLQRKDGRLLALLDSGQ------ARCELPLGMQDAGLEDREVILGIRPEQIILANGE 297
           I   ++   G ++ +   G+      ARC    G          VILG+RPE++ +A  E
Sbjct: 253 IAGTVESVSGDVVQVAAHGRSLALPAARCRTTSG---------PVILGVRPEKVRIAKTE 303

Query: 298 A 298
           A
Sbjct: 304 A 304


Lambda     K      H
   0.319    0.138    0.393 

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: 14
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 ( 7.4 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