GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1897 in Desulfovibrio vulgaris Hildenborough

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 209027 DVU0098 polyamine ABC transporter, ATP-binding protein

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



>MicrobesOnline__882:209027
          Length = 368

 Score =  216 bits (551), Expect = 6e-61
 Identities = 120/290 (41%), Positives = 175/290 (60%), Gaps = 10/290 (3%)

Query: 4   LELRNVNKTYGPGLPDT--LKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGA 61
           +ELR V K +     DT  L NI+L+I +GEFL L+GPSGCGK+T++  I+G E    G 
Sbjct: 8   IELRGVTKNF----EDTCALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGV 63

Query: 62  ILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSK 121
           I +    +    P+ R +  VFQ+YAL+P MSVR+N+ FGL++++ P  EI   V    +
Sbjct: 64  ITLKGQRMDDAPPEARQVNTVFQNYALFPHMSVRENVGFGLRMQRRPKDEIARRVHDALR 123

Query: 122 LLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLM 181
           ++ +E    R+P QLSGGQQQRVA+ RA+   P + L DEP S LD KLR +M+ E+K +
Sbjct: 124 MVHLEAHADRRPRQLSGGQQQRVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHL 183

Query: 182 HQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPM 241
            ++L  T V+VTHDQ EA  + D+V VM DG I+Q G+P++IY  PANL+VA F+G   +
Sbjct: 184 QRQLGITFVFVTHDQEEAFAMSDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFVGEINI 243

Query: 242 NFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQI 291
               +     DG   A+++        P+  Q       +V + +RPE +
Sbjct: 244 LNAVIAANHGDGLYDAVIEG----VTFPIRSQRTFAPGDKVNVLLRPEDL 289


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: 390
Number of extensions: 11
Number of successful extensions: 1
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: 368
Length adjustment: 30
Effective length of query: 356
Effective length of database: 338
Effective search space:   120328
Effective search space used:   120328
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