GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Pseudomonas putida KT2440

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate PP_1018 PP_1018 mannose/glucose ABC transporter - ATP binding subunit

Query= reanno::Smeli:SM_b21106
         (365 letters)



>FitnessBrowser__Putida:PP_1018
          Length = 384

 Score =  320 bits (821), Expect = 3e-92
 Identities = 173/370 (46%), Positives = 236/370 (63%), Gaps = 12/370 (3%)

Query: 1   MAPVTLKKLVKRYGA--LEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGG 58
           MA + L+ + K YG+   + +  I L +KD EF+ LVGPSGCGKST +  IAGLE+++GG
Sbjct: 1   MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60

Query: 59  AIEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAA 118
           AI I  + V+ + P+ R+I+MVFQSYALYP M+V EN+ F LKI   P   I   VA  A
Sbjct: 61  AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA 120

Query: 119 AILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKK 178
            +L + HLL R+P+QLSGGQ+QRVAMGRA+ R+P ++LFDEPLSNLDAKLR ++RTE+K 
Sbjct: 121 KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 179 LHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPP 238
           +H R++ T +YVTHDQ+EAMTL D++ +M+DG I+Q GTP+ ++  PA +FVA FIGSPP
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPP 240

Query: 239 MNMEEAVLT--DGKLAF---ASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHA 293
           MN     L   DG+L     +  A   LP    +   EG+++  G+RP+ +      L A
Sbjct: 241 MNFIPVRLARQDGRLLALLDSGQARCELPLGEAADALEGREIILGIRPEQI-----ALGA 295

Query: 294 GDADAVHEIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLARAH 353
            D + +  I   V +TEP G + LVF   N      R+      R G+ + + FD AR  
Sbjct: 296 ADGNGLPAIRAEVQVTEPTGPDLLVFVTLNQTKVCCRLAPDVACRVGDTLNLQFDPARVL 355

Query: 354 LFDGETGRAL 363
           LFD   G  L
Sbjct: 356 LFDAANGERL 365


Lambda     K      H
   0.320    0.137    0.397 

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: 405
Number of extensions: 15
Number of successful extensions: 2
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: 365
Length of database: 384
Length adjustment: 30
Effective length of query: 335
Effective length of database: 354
Effective search space:   118590
Effective search space used:   118590
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: 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