GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Phaeobacter inhibens BS107

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC

Query= uniprot:Q6MNM2
         (347 letters)



>FitnessBrowser__Phaeo:GFF262
          Length = 348

 Score =  295 bits (754), Expect = 2e-84
 Identities = 161/348 (46%), Positives = 220/348 (63%), Gaps = 9/348 (2%)

Query: 1   MAKIQFSNIKKSF-GSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGT 59
           MA++  ++++K +    + +      I  GEF+VLVGPSGCGKSTLLR +AGLE    GT
Sbjct: 1   MAQVTLNSVRKVYPNGVEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEGT 60

Query: 60  ISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISE 119
           + I  + +N+++P +RDIAMVFQ+YALYPHMTV +N+ +GLK +    AEI ++V E ++
Sbjct: 61  LEIGDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQKVAEAAK 120

Query: 120 LLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRL 179
           +L ++  LDRKP +LSGGQRQRVA+GRA+ R   + LFDEPLSNLDA LR+QMR+EIK L
Sbjct: 121 MLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKAL 180

Query: 180 HHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEM 239
                 T IYVTHDQ+EA T+ DRI VL  G IEQIGTPSEIYH P + F+A+F+G+P M
Sbjct: 181 QRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPPM 240

Query: 240 NFLEGAVLE-KIPWPEARKADQILGIRPDAFALNQGPLGTQEVALGDFQIDIS--ENLGG 296
           N L+  +   ++  P+      +      A  L   P   Q VA G   ID+   E LG 
Sbjct: 241 NLLDATIANGQVTLPDGVSMGALDTSAQGAVKLGIRPEDVQLVAEGGLAIDVELIEELGA 300

Query: 297 QQMLHGTLAGN--NVRILVDSMDNFSMKQTLPLKIDLTKAHLFDKKTG 342
            ++LHG L G    + +L D   +    Q   + +D     LFD ++G
Sbjct: 301 HRLLHGKLGGQPFTIHVLKDIPVDPGTHQ---ISVDPAAICLFDAESG 345


Lambda     K      H
   0.318    0.136    0.383 

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: 304
Number of extensions: 7
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: 347
Length of database: 348
Length adjustment: 29
Effective length of query: 318
Effective length of database: 319
Effective search space:   101442
Effective search space used:   101442
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: 49 (23.5 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