GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Thiothrix lacustris DSM 21227

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_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  279 bits (714), Expect = 7e-80
 Identities = 169/374 (45%), Positives = 228/374 (60%), Gaps = 46/374 (12%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M  L+L N+ K Y   K ++++  +L+I   EFIVFVGPSGCGKST LRMIAGLE I  G
Sbjct: 1   MAFLELKNVDKYY--GKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGG 58

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            L +D + + +  P  RD+AMVFQ+YALYPHM+V ENM+F L+L K     I ++V  AA
Sbjct: 59  QLILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAA 118

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
           + L LT +L+R P  LSGGQRQRVA+GR+IVR  KVFL DEPLSNLDA LR   R EIA 
Sbjct: 119 DKLNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIAS 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +HR +GATT+YVTHDQ EAMTLADR+V++            G IEQ+GTP ELY++P N+
Sbjct: 179 LHRELGATTVYVTHDQVEAMTLADRVVVLRD----------GIIEQVGTPLELYDQPINR 228

Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDI 300
           FVA FIG P MN     V    L  Q                   +  +   +GIRPE +
Sbjct: 229 FVARFIGMPQMN-----VAPASLFGQ-------------------FPAQVAEVGIRPEHL 264

Query: 301 SSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTE----FTARVNARDSHSPGEKV 356
              Q+V     +  +   +++ E LG+E++++V+    +       R+  R +   G++V
Sbjct: 265 ---QMVSP--EDGLLAGKVVLVEALGNETLVHVRPDKVQLEEPLIVRLYGRTTVHVGDRV 319

Query: 357 QLTFNIAKG-HFFD 369
            L ++ +K  H+FD
Sbjct: 320 GLKWDDSKHIHYFD 333


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: 327
Number of extensions: 13
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: 348
Length adjustment: 29
Effective length of query: 348
Effective length of database: 319
Effective search space:   111012
Effective search space used:   111012
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 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