GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Pseudomonas fluorescens FW300-N2C3

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 AO356_05180 AO356_05180 sugar ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05180
          Length = 386

 Score =  306 bits (785), Expect = 5e-88
 Identities = 173/384 (45%), Positives = 243/384 (63%), Gaps = 27/384 (7%)

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

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

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
           ++L +   L RKP  LSGGQ+QRVAMGRA+ R  K++L DEPLSNLDAKLRV MR E+  
Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +H+R+  TT+YVTHDQ EAMTL D++ +M            G I+Q GTP+++Y  PAN 
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKD----------GIIQQFGTPKDIYTNPANL 230

Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLA-LPQGQEKI-----LEEKGYLGKKVTLG 294
           FVA FIGSP MNF  +     RL  +DG  LA L  GQ +      +++ G   ++V LG
Sbjct: 231 FVASFIGSPPMNFIPL-----RLQRKDGRLLALLDSGQARCELPMGMQDAGLEDREVILG 285

Query: 295 IRPEDISSDQIVHETFPNA--SVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSP 352
           +RPE I    ++  + PN   ++ A++ V+E  G +++++V    T+   R+    +   
Sbjct: 286 MRPEQI----MLAGSEPNGLPTIRAEVQVTEPTGPDTLVFVSLNDTKVCCRLAPDVAPQV 341

Query: 353 GEKVQLTFNIAKGHFFDLETEKRI 376
           GE + L F+ +K   FD ++ +R+
Sbjct: 342 GETLTLQFDPSKVLLFDAQSGERL 365


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: 388
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: 377
Length of database: 386
Length adjustment: 30
Effective length of query: 347
Effective length of database: 356
Effective search space:   123532
Effective search space used:   123532
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