GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Pseudomonas putida KT2440

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate PP_1018 PP_1018 mannose/glucose ABC transporter - ATP binding subunit

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__Putida:PP_1018
          Length = 384

 Score =  310 bits (795), Expect = 3e-89
 Identities = 176/383 (45%), Positives = 241/383 (62%), Gaps = 23/383 (6%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M TL+L N+ K Y +    ++++  L I D EF++ VGPSGCGKST +  IAGLE IT G
Sbjct: 1   MATLELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGG 60

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            + ID++ ++  SPKDRDIAMVFQ+YALYP MSV EN+ FGLK+RK  +  I++ V   A
Sbjct: 61  AILIDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVA 120

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
           ++L +   L RKPA LSGGQ+QRVAMGRA+ R  K++L DEPLSNLDAKLRV MR E+  
Sbjct: 121 KLLQIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +H+R+  TT+YVTHDQ EAMTL D++ +M            G I+Q GTPQ++YN+PAN+
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKD----------GIIQQFGTPQQIYNDPANQ 230

Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLA-LPQGQEKILEEKGYL-----GKKVTLG 294
           FVA FIGSP MNF  V     RL  QDG  LA L  GQ +     G       G+++ LG
Sbjct: 231 FVASFIGSPPMNFIPV-----RLARQDGRLLALLDSGQARCELPLGEAADALEGREIILG 285

Query: 295 IRPEDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGE 354
           IRPE I+         P  ++ A++ V+E  G + +++V    T+   R+    +   G+
Sbjct: 286 IRPEQIALGAADGNGLP--AIRAEVQVTEPTGPDLLVFVTLNQTKVCCRLAPDVACRVGD 343

Query: 355 KVQLTFNIAKGHFFDLETEKRIN 377
            + L F+ A+   FD    +R++
Sbjct: 344 TLNLQFDPARVLLFDAANGERLH 366


Lambda     K      H
   0.318    0.135    0.379 

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: 379
Number of extensions: 18
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: 377
Length of database: 384
Length adjustment: 30
Effective length of query: 347
Effective length of database: 354
Effective search space:   122838
Effective search space used:   122838
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: 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