GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Sm in Rhodobacter viridis JA737

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_110804244.1 C8J30_RS03245 ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_003217355.1:WP_110804244.1
          Length = 332

 Score =  285 bits (730), Expect = 1e-81
 Identities = 170/371 (45%), Positives = 220/371 (59%), Gaps = 44/371 (11%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M  + L  + KR+ + +   +   +L IHD EF+VFVGPSGCGKST LR+IAGLED++ G
Sbjct: 1   MGEIVLKGVTKRFGDVE--VIPPIDLAIHDGEFVVFVGPSGCGKSTLLRLIAGLEDVSGG 58

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            + ID K   + +P DR +AMVFQ+YALYPHMSV +N+AF LK+ K    +I  +V  AA
Sbjct: 59  KIEIDGKDATETAPSDRGLAMVFQSYALYPHMSVKKNIAFPLKMAKLPPAEIEAKVQAAA 118

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
           ++L L+ +L+RKP  LSGGQRQRVA+GRAIVR  + FL DEPLSNLDA LRV MR EI++
Sbjct: 119 KVLNLSAYLDRKPGQLSGGQRQRVAIGRAIVRSPEAFLFDEPLSNLDAALRVNMRLEISE 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +H  +  T IYVTHDQ EAMT+AD+IV++ A          GRIEQ+G+P ELY  P N+
Sbjct: 179 LHHTLKTTMIYVTHDQVEAMTMADKIVVLQA----------GRIEQVGSPLELYRTPRNR 228

Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDI 300
           FVAGFIGSP MNF E              + A   G   I             GIRPE I
Sbjct: 229 FVAGFIGSPKMNFIEG-------------AEAAKHGAHAI-------------GIRPEHI 262

Query: 301 SSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQLTF 360
                   +         + VSE LGS++ L+V         R         G+ V L+ 
Sbjct: 263 ------RISTTEGMWKGTVGVSEHLGSDTFLHVTTEHGLLNVRAGGEVDLHHGDSVFLSP 316

Query: 361 NIAKGHFFDLE 371
           ++A+ H FD E
Sbjct: 317 DMAQLHRFDKE 327


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: 310
Number of extensions: 13
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 377
Length of database: 332
Length adjustment: 29
Effective length of query: 348
Effective length of database: 303
Effective search space:   105444
Effective search space used:   105444
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