GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Phaeacidiphilus oryzae TH49

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 WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  317 bits (812), Expect = 3e-91
 Identities = 178/389 (45%), Positives = 239/389 (61%), Gaps = 33/389 (8%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M T+  D   + YP     +V+  +L+I D EF+V VGPSGCGKST+LRM+AGLED+  G
Sbjct: 1   MATVTYDKATRIYPGGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNG 60

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            + I ++ +    PKDRDIAMVFQNYALYPHM+V +NM F LK+    K +I  +V EAA
Sbjct: 61  AIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAA 120

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
           +IL LTEFL+RKP  LSGGQRQRVAMGRAIVR+ +VFLMDEPLSNLDAKLRV+ R +IA 
Sbjct: 121 KILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAG 180

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           + RR+G TT+YVTHDQ EAMT+ DR+ ++            G ++Q+ TP+ +Y+ PAN 
Sbjct: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKD----------GLLQQVDTPRNMYDRPANL 230

Query: 241 FVAGFIGSPAMNFFEVTV--------EKERLVNQDGLSLALPQGQEKILEEKGYLGKKVT 292
           FVAGFIGSPAMN  EV +        E    V++D +  A   G            K VT
Sbjct: 231 FVAGFIGSPAMNLVEVPITDGGVKFGESVVQVSRDAVGEAANAGD-----------KTVT 279

Query: 293 LGIRPEDISSDQIVHETFPNASVTADILVSELLGSESMLY--VKFG--STEFTARVNARD 348
           +G+RPE +           +  +   + V E LG++  +Y   K G  + +   RV  RD
Sbjct: 280 VGVRPEHLDIVGGTEGGGEDKGLAVTVNVVEELGADGYVYGSAKVGTETIDLVVRVGGRD 339

Query: 349 SHSPGEKVQLTFNIAKGHFFDLETEKRIN 377
               G+++++     + H F   T KR++
Sbjct: 340 IPMKGDQLRVVPRAGETHVFSTSTGKRLS 368


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: 382
Number of extensions: 20
Number of successful extensions: 4
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: 369
Length adjustment: 30
Effective length of query: 347
Effective length of database: 339
Effective search space:   117633
Effective search space used:   117633
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 Apr 09 2024. 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