GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Dyella japonica UNC79MFTsu3.2

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein

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



>FitnessBrowser__Dyella79:N515DRAFT_1562
          Length = 384

 Score =  201 bits (510), Expect = 4e-56
 Identities = 147/388 (37%), Positives = 205/388 (52%), Gaps = 29/388 (7%)

Query: 3   TLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAI 62
           +L +R + + YG      L +  L I +GEF+ L+GPSG GKS+L+  +AGL+    G +
Sbjct: 2   SLSIRQLTRRYGAFA--ALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDV 59

Query: 63  LVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVA-RVSK 121
           L D  D+  +  + RDI +VFQ YAL+P M+V DNIAFGL++R         ++A RV  
Sbjct: 60  LRDGTDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVED 119

Query: 122 LL---QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEM 178
           LL   Q+E L  R P QLSGGQ+QRVA+ RALA  P + L DEP   LDA++R  +R  +
Sbjct: 120 LLRRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWL 179

Query: 179 KLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGS 238
           + + + L  TTV VTHDQ EA+ L D+V VM  G I+Q G P +IY  PA  FV  F+G 
Sbjct: 180 RDLQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVGR 239

Query: 239 PPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEA 298
                   R++    R    L     + ELP       L  RE+   +RPE + LA   +
Sbjct: 240 AN------RIRGHVERDRLHLGGHSFQGELP-----GDLAGREIEAWLRPEHLALA---S 285

Query: 299 NGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRL---APDVAP---AVGETLTLQFDPA 352
            GL      +Q  +  GP     + ++   +       A +VA    A+GE +TLQ  P 
Sbjct: 286 RGLGGWTGRLQHLDLAGPVARARLAMHGDGLVLDAEWNAAEVAAHGLAIGEVVTLQ--PR 343

Query: 353 KVLLFDAKTGERLGVAGVP-KAEAHADN 379
           +  LF    G    +  VP  A  HAD+
Sbjct: 344 EFTLFADVPGGVRRLRFVPAPAGPHADS 371


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: 371
Number of extensions: 15
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: 384
Length adjustment: 30
Effective length of query: 356
Effective length of database: 354
Effective search space:   126024
Effective search space used:   126024
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