GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Halomonas xinjiangensis TRM 0175

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_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  313 bits (802), Expect = 5e-90
 Identities = 182/377 (48%), Positives = 242/377 (64%), Gaps = 31/377 (8%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M +++L  + K Y      +V+  +L+I D EF+V VGPSGCGKST LRM+AGLE IT+G
Sbjct: 1   MASIQLTGLKKTYAGNVE-AVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDG 59

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            L IDD+++ND  P +RDIAMVFQNYALYPHM+V+ N+A+GLK R  K+++I +RVH+AA
Sbjct: 60  TLKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAA 119

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
            +L +  FLERKP  LSGGQRQRVAMGRA+VR+   FL DEPLSNLDAKLRV MR EI +
Sbjct: 120 AMLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQ 179

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           + RR+  T++YVTHDQ EA+TL DR+V+++           G IEQ+GTP E+Y +PA+ 
Sbjct: 180 LQRRLKTTSLYVTHDQLEALTLGDRLVVLNG----------GSIEQVGTPMEVYEKPASM 229

Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDI 300
           FVA FIGSPAMN   V   +ER  N  GL   L    +              +GIRP+D+
Sbjct: 230 FVATFIGSPAMNMLPVAYLRERGAN--GLLDHLAADTD-------------VIGIRPDDL 274

Query: 301 SSDQIVHETFPNASVTADILVSELLGSESMLYVKF-GSTEFTA-RVNARDSHSPGEKVQL 358
              +I      +  VT  + + E  G+ES LYV   GS + T  R +AR   + GE ++ 
Sbjct: 275 ---RIEAPDEDHLVVTGTVELFEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMRF 331

Query: 359 TFNIAKGHFFDLETEKR 375
               +  H F+  + KR
Sbjct: 332 HVLPSALHPFNQASGKR 348


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: 343
Number of extensions: 18
Number of successful extensions: 2
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: 354
Length adjustment: 30
Effective length of query: 347
Effective length of database: 324
Effective search space:   112428
Effective search space used:   112428
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.

Links

Downloads

Related tools

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