GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Paraburkholderia bryophila 376MFSha3.1

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate H281DRAFT_03749 H281DRAFT_03749 carbohydrate ABC transporter ATP-binding protein, CUT1 family

Query= uniprot:Q6MNM2
         (347 letters)



>FitnessBrowser__Burk376:H281DRAFT_03749
          Length = 360

 Score =  296 bits (758), Expect = 5e-85
 Identities = 162/363 (44%), Positives = 217/363 (59%), Gaps = 28/363 (7%)

Query: 1   MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60
           MA +Q S I K +G   V+ GIDL I  GEF+VLVGPSGCGKSTL+R +AGLE    G +
Sbjct: 1   MAAVQLSGIFKRYGDTQVVHGIDLHIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDL 60

Query: 61  SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120
            I G + N++ PQ R+I+MVFQSYALYPH++V EN+ FG +++  + A    R+   +++
Sbjct: 61  MIGGTRANNLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESPANFKPRIEAAAKM 120

Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180
           L +   LDR P+ LSGGQRQRVA+GRA+ R+  + LFDEPLSNLDA LR QMR EIK LH
Sbjct: 121 LNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKALH 180

Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240
              K+T+IYVTHDQ+EA T+ DRI V+  G IEQIG P E+Y  P N F+A+F+GSP MN
Sbjct: 181 QRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSMN 240

Query: 241 FLEGA--------------------VLEKIPWPEARKADQILGIRPDAF-ALNQGPLGTQ 279
           F EG                     VLE  P      A   LG+RP+    + Q P  T 
Sbjct: 241 FAEGVLVNRTQGSGLALKLADGGEIVLEGAPASATVGAKVTLGVRPEHIETITQTPDVT- 299

Query: 280 EVALGDFQIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFDK 339
                  Q+++ E  G +  L+G + G+   +           + + L++     HLFD 
Sbjct: 300 ------MQVEVVEPTGAETHLYGKIGGDTWCVTTRQRSKVEPGERVTLRLPAAHIHLFDT 353

Query: 340 KTG 342
           ++G
Sbjct: 354 ESG 356


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: 325
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: 347
Length of database: 360
Length adjustment: 29
Effective length of query: 318
Effective length of database: 331
Effective search space:   105258
Effective search space used:   105258
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