GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Phyllobacterium brassicacearum STM 196

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_106712952.1 CU102_RS20485 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_003010955.1:WP_106712952.1
          Length = 356

 Score =  329 bits (843), Expect = 8e-95
 Identities = 189/378 (50%), Positives = 236/378 (62%), Gaps = 25/378 (6%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M ++ + N+ K Y      S    +L I D EF+V VGPSGCGKST LRMIAGLE+I+ G
Sbjct: 1   MASVTISNVQKNYGAMNVLSA--VDLSIADGEFVVLVGPSGCGKSTLLRMIAGLEEISAG 58

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            + I D+++ND +PKDRDIAMVFQ+YALYPHM V ENM F L LRK  KD I  RV  AA
Sbjct: 59  EIRIGDRVVNDVAPKDRDIAMVFQSYALYPHMDVAENMGFSLTLRKTAKDLIMNRVGNAA 118

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
           + LGL  FLER P  LSGGQRQRVAMGRAIVRD KVFL DEPLSNLDAKLRV MR EI  
Sbjct: 119 KRLGLDVFLERLPRQLSGGQRQRVAMGRAIVRDPKVFLFDEPLSNLDAKLRVHMRTEIKA 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +H+++  T++YVTHDQ EAMT+ADRIV+M            G I+Q+GTP ELY+ PAN 
Sbjct: 179 LHQQLKTTSVYVTHDQVEAMTMADRIVVMHD----------GVIQQVGTPLELYDHPANL 228

Query: 241 FVAGFIGSPAMNFFEVTVEKE--RLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPE 298
           FVAGFIGSP MNF    V ++  ++  +      +P   E  +E+    G +VT+G+RPE
Sbjct: 229 FVAGFIGSPGMNFLPAVVSRQGAKVAAELADGQMIPLRPELRVED----GDRVTVGVRPE 284

Query: 299 DISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQL 358
           +I       E   + ++TA I V E LG  +  Y K    +       R    PG+ + L
Sbjct: 285 NI-------EVGGSDALTAKIEVIEPLGLSTQFYAKLADQQICIFAMGRTDRGPGDTISL 337

Query: 359 TFNIAKGHFFDLETEKRI 376
             N    H F  +T  R+
Sbjct: 338 GINPTAVHVFHAKTGIRL 355


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: 358
Number of extensions: 13
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: 356
Length adjustment: 30
Effective length of query: 347
Effective length of database: 326
Effective search space:   113122
Effective search space used:   113122
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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