GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Phaeobacter inhibens BS107

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

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



>FitnessBrowser__Phaeo:GFF1915
          Length = 363

 Score =  312 bits (799), Expect = 1e-89
 Identities = 166/356 (46%), Positives = 233/356 (65%), Gaps = 21/356 (5%)

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

Query: 76  DRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLLQIEHLLSRKPGQ 135
           DR +AMVFQSYALYP M+VR N+AFGL++ K+P AE D+ V   +++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 QIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNFIPLRLQRKDGRL 255
           Q+EA+TL D++AVMKDG++QQ  +P++IY  PAN +VA F+G P MNF+       +G  
Sbjct: 203 QVEALTLADRIAVMKDGVVQQLDSPEEIYRRPANRYVAQFVGLPSMNFV-------NG-- 253

Query: 256 LALLDSGQARCE-LPLGMQDAGLED-----REVILGIRPEQIILANGEANGLPTIRAEVQ 309
             + +SG  + E   L +    L        EV +GIRPE +  AN  A G      +V 
Sbjct: 254 -VVTESGAIQTEDFELALDQCNLASTPAPGTEVEIGIRPEHVHPAN--AGG---FMLDVG 307

Query: 310 VTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDAKTGERL 365
           + E  G + L++  + +T +  R  PD     G+ + +   P    +F AKTG R+
Sbjct: 308 MVELLGSERLIWGKVGNTSIVMRDDPDTTIRSGDQVRINLKPGAFSVFSAKTGLRI 363


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: 369
Number of extensions: 13
Number of successful extensions: 3
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 ( 7.4 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 Sep 17 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