GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate H281DRAFT_03749 H281DRAFT_03749 carbohydrate ABC transporter ATP-binding protein, CUT1 family

Query= reanno::Smeli:SMc04256
         (361 letters)



>FitnessBrowser__Burk376:H281DRAFT_03749
          Length = 360

 Score =  298 bits (762), Expect = 2e-85
 Identities = 165/364 (45%), Positives = 225/364 (61%), Gaps = 8/364 (2%)

Query: 1   MTSVSVRDLSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQI 60
           M +V +  +   +G   V+  ++L ID GEF+VL+G SGCGKSTL+  +AGL ++S G +
Sbjct: 1   MAAVQLSGIFKRYGDTQVVHGIDLHIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDL 60

Query: 61  FIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEI 120
            I         P+ R I MVFQSYALYP ++V +N++FG ++ K  PA  + R++ A+++
Sbjct: 61  MIGGTRANNLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESPANFKPRIEAAAKM 120

Query: 121 LQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLH 180
           L +   L R P  LSGGQRQRVA+GRA+VR+  +FLFDEPLSNLDAKLR ++R EIK LH
Sbjct: 121 LNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKALH 180

Query: 181 QSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMN 240
           Q LKNT+IYVTHDQIEA+T+ADRI VM +G I+Q+  P+ +Y+ P NLFVA F+GSPSMN
Sbjct: 181 QRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSMN 240

Query: 241 FFRGEVEPK---DGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGE 297
           F  G +  +    G +   A G    +   PA   +  G KV LG+RPEH+   E     
Sbjct: 241 FAEGVLVNRTQGSGLALKLADGGEIVLEGAPASATV--GAKVTLGVRPEHI---ETITQT 295

Query: 298 PTHQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYPPGSTVRLSFDMGVASIFDAES 357
           P     V++ EP GA+  L+    G +  V    + +  PG  V L        +FD ES
Sbjct: 296 PDVTMQVEVVEPTGAETHLYGKIGGDTWCVTTRQRSKVEPGERVTLRLPAAHIHLFDTES 355

Query: 358 ENRL 361
             RL
Sbjct: 356 GRRL 359


Lambda     K      H
   0.320    0.137    0.392 

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: 363
Number of extensions: 14
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: 361
Length of database: 360
Length adjustment: 29
Effective length of query: 332
Effective length of database: 331
Effective search space:   109892
Effective search space used:   109892
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 (21.8 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