GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Pseudomonas fluorescens GW456-L13

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate PfGW456L13_4204 ABC transporter, ATP-binding protein

Query= TCDB::P54933
         (332 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4204
          Length = 329

 Score =  246 bits (627), Expect = 7e-70
 Identities = 133/298 (44%), Positives = 191/298 (64%), Gaps = 7/298 (2%)

Query: 1   MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI 60
           M  ++++++QK F    V   ++ +I+ GEFV  +GPSGCGKSTLLR IAGL  V  G+I
Sbjct: 1   MSYVSVQHLQKSFAGTTVFSDINCEIQKGEFVTLLGPSGCGKSTLLRCIAGLTSVDGGKI 60

Query: 61  MIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI 120
           ++DG D   + P KRG+ MVFQSYAL+P+MTV++N+AF LRM K+   +  +RV+   K+
Sbjct: 61  LLDGADIVPVSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVNADDSRKRVAEVLKL 120

Query: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH 180
           + L ++  R P QLSGGQ QRVA+ R++V  P   L DEPLS LDA +R ++R +I ++ 
Sbjct: 121 VELNDFAARYPHQLSGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKHLREQIRQIQ 180

Query: 181 QSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMN 240
           + L  T I+VTHDQ EA+TM+D+I ++N G+I Q G   TLY  P ++F AGFIG+   N
Sbjct: 181 RELGLTTIFVTHDQEEALTMSDRIFLMNQGKIVQSGDAETLYTAPVDVFAAGFIGN--YN 238

Query: 241 LIEGPEAAK----HGATTIGIRPEHIDLSREAGAWEGEVGVSEHLGSDTFLHVHVAGM 294
           L++   A+K         I IRPE I+LS + G  + +V     LG+     V   G+
Sbjct: 239 LLDADSASKLLQRPINKRIAIRPEAIELSLD-GELDAQVRSHSLLGNVIRYRVEARGV 295


Lambda     K      H
   0.320    0.137    0.400 

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: 258
Number of extensions: 8
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: 332
Length of database: 329
Length adjustment: 28
Effective length of query: 304
Effective length of database: 301
Effective search space:    91504
Effective search space used:    91504
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