GapMind for catabolism of small carbon sources

 

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

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

Query= reanno::Smeli:SM_b20002
         (358 letters)



>FitnessBrowser__Burk376:H281DRAFT_03749
          Length = 360

 Score =  348 bits (894), Expect = e-100
 Identities = 185/362 (51%), Positives = 245/362 (67%), Gaps = 9/362 (2%)

Query: 1   MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60
           M+ +QLS + K YG  +V+ G+DL I  GEFVV VGPSGCGKSTL+RM+AGLEEIS GDL
Sbjct: 1   MAAVQLSGIFKRYGDTQVVHGIDLHIDDGEFVVLVGPSGCGKSTLMRMVAGLEEISGGDL 60

Query: 61  TIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHI 120
            I   R N++ P +R I+MVFQSYALYPH++V EN+ F  R      A  + R+  AA +
Sbjct: 61  MIGGTRANNLAPQQRNISMVFQSYALYPHLSVYENIAFGPRIRKESPANFKPRIEAAAKM 120

Query: 121 LELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH 180
           L LG  LDR P+ LSGGQRQRVA+GRA+VR P +FLFDEPLSNLDA+LRV MR EI  LH
Sbjct: 121 LNLGGYLDRLPRALSGGQRQRVAMGRAVVREPSLFLFDEPLSNLDAKLRVQMRTEIKALH 180

Query: 181 KQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMN 240
           ++L  T++YVTHDQ+EAMT+AD+IVVM AG +EQ+G PL+LYD PANLFVA F+GSP MN
Sbjct: 181 QRLKNTVIYVTHDQIEAMTMADRIVVMNAGRIEQIGRPLELYDHPANLFVASFLGSPSMN 240

Query: 241 FLKGVIEIDEDQAYA---RLPDYGDAKIP-VTLQAAAGTAVTIGIRPEHFDEAGPAA-LD 295
           F +GV+ ++  Q      +L D G+  +      A  G  VT+G+RPEH +       + 
Sbjct: 241 FAEGVL-VNRTQGSGLALKLADGGEIVLEGAPASATVGAKVTLGVRPEHIETITQTPDVT 299

Query: 296 LAIDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGE-GK 354
           + ++++E  G ET  Y +    G+   V T+    ++ G+R+T R     + +FD E G+
Sbjct: 300 MQVEVVEPTGAETHLYGKI--GGDTWCVTTRQRSKVEPGERVTLRLPAAHIHLFDTESGR 357

Query: 355 RL 356
           RL
Sbjct: 358 RL 359


Lambda     K      H
   0.321    0.139    0.396 

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: 391
Number of extensions: 11
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: 358
Length of database: 360
Length adjustment: 29
Effective length of query: 329
Effective length of database: 331
Effective search space:   108899
Effective search space used:   108899
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