GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Phaeobacter inhibens BS107

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate GFF1915 PGA1_c19470 ABC transporter, ATP-binding protein

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



>FitnessBrowser__Phaeo:GFF1915
          Length = 363

 Score =  319 bits (818), Expect = 7e-92
 Identities = 165/350 (47%), Positives = 234/350 (66%), Gaps = 9/350 (2%)

Query: 16  GLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIMIGDQDVSGMSPK 75
           G  + LK++ L I++GEFL+L+G SGCGKSTL+N IAGL+  T G I I D++V+   PK
Sbjct: 23  GAVEVLKSLNLDIQKGEFLVLLGASGCGKSTLLNTIAGLQEATEGQIWINDENVTWREPK 82

Query: 76  DRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLLQIEHLLNRKPGQ 135
           DR +AMVFQSYALYP M+VR N+ FGL++ K+P+A+ D  V   A++LQ+E LL+R+PG+
Sbjct: 83  DRGLAMVFQSYALYPKMTVRGNLAFGLRMNKVPKAEADKLVDEAARVLQLEELLDRRPGE 142

Query: 136 LSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHD 195
           LSGGQ+QRVA+GRAL R+  ++LFDEPLSNLDAKLR E+R E+K +HQ L  T +YVTHD
Sbjct: 143 LSGGQRQRVAIGRALVRKVDVFLFDEPLSNLDAKLRAELRVELKRLHQELGATMIYVTHD 202

Query: 196 QIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNFVPLRLQRKDGRL 255
           Q+EA+TL D++AVMKDG++QQ  +P+EIY  PAN++VA F+G P MNFV   +       
Sbjct: 203 QVEALTLADRIAVMKDGVVQQLDSPEEIYRRPANRYVAQFVGLPSMNFVNGVVTESGAIQ 262

Query: 256 VALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDSASSIRAEVQVTEPTG 315
               +    +C LA +T   G E   V +G+RPE +  A     +A     +V + E  G
Sbjct: 263 TEDFELALDQCNLA-STPAPGTE---VEIGIRPEHVHPA-----NAGGFMLDVGMVELLG 313

Query: 316 PDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDANTGERL 365
            + L++ ++ +T +  R  PD   + G+ + +   P    +F A TG R+
Sbjct: 314 SERLIWGKVGNTSIVMRDDPDTTIRSGDQVRINLKPGAFSVFSAKTGLRI 363


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: 339
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: 363
Length adjustment: 30
Effective length of query: 356
Effective length of database: 333
Effective search space:   118548
Effective search space used:   118548
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 Sep 17 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