GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Desulfacinum infernum DSM 9756

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_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_900129305.1:WP_073038605.1
          Length = 368

 Score =  367 bits (943), Expect = e-106
 Identities = 198/381 (51%), Positives = 263/381 (69%), Gaps = 19/381 (4%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M  +KLD + KR+   K++ V +F L + DKEF+V VGPSGCGKSTTLRMIAGLE++T G
Sbjct: 1   MAEIKLDQVNKRFK--KNWVVRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVTSG 58

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            + I  +++N   PKDRDIAMVFQ+YALYPHM+VY+NMAFGL  R   +D+I++RV +AA
Sbjct: 59  EISIGGRVVNHVPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEIDRRVKQAA 118

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
           EILG+++ L+R+PA LSGGQRQRVAMGRAIVRD + FL DEPLSNLDAKLRV MRAE+AK
Sbjct: 119 EILGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQMRAELAK 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +H R+ +T +YVTHDQ EAMTLADRIV+M            G+I Q+G P E+Y  PAN+
Sbjct: 179 LHERLQSTIVYVTHDQIEAMTLADRIVVMKD----------GKIMQVGPPLEVYERPANR 228

Query: 241 FVAGFIGSPAMNFFEV-TVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPED 299
           FVAGFIGSP+MNF +V  VE+   +  DG S  L   + +    +G++ + V  GIRPED
Sbjct: 229 FVAGFIGSPSMNFLDVRLVEEAGDLWVDGESFRLKVPRHRAPAFRGHVNRPVIFGIRPED 288

Query: 300 IS---SDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKV 356
           +     D +     P   + A++ V E +GSE ++    GS  FTAR++   +    + +
Sbjct: 289 VKERPGDALPEGVEP---LRAEVDVREPIGSEVIITATVGSHAFTARISPNVAVRVHDPI 345

Query: 357 QLTFNIAKGHFFDLETEKRIN 377
            L  N+ K H FD E+E+ +N
Sbjct: 346 DLAVNMNKMHLFDPESEQALN 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: 419
Number of extensions: 18
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: 368
Length adjustment: 30
Effective length of query: 347
Effective length of database: 338
Effective search space:   117286
Effective search space used:   117286
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