GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Marinobacter adhaerens HP15

Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Marino:GFF3011
          Length = 372

 Score =  326 bits (835), Expect = 7e-94
 Identities = 180/386 (46%), Positives = 248/386 (64%), Gaps = 38/386 (9%)

Query: 1   MAKVRLEHVWKRFGKVV--AVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEG 58
           M+++ L  + K +  V    +K  +++   GEF++ VGPSGCGK+T +  IAGLE I++G
Sbjct: 1   MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60

Query: 59  NIYIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAA 118
           +I +  + ++ + PKDRDIAMVFQ+YALYP M+V EN+AFGL++R  PK EID+ V+  A
Sbjct: 61  SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120

Query: 119 RILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAK 178
            +L+I  L+N+KP  LSGGQ+QRVAMGRA+ R P+++L DEPLSNLDAKLRVEMR EI K
Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180

Query: 179 LQRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPS 238
           L +RL  T +YVTHDQ+EAMTL  RI V+KDGE+QQ+ TP  +YD P N FVAGF+GSP+
Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240

Query: 239 MNFVRAGVEV------------QGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRP 286
           M+FV   VE              G  V L  P F           L    GK+V LG+RP
Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEF-----------LADRVGKKVILGIRP 289

Query: 287 EHLGLKGYTTIPEEEN-----VLRGE--VEVVEPLGAETEIHVAVNGTLLVAKVDGHAPV 339
           EH+      T P+++      V +GE  +EV EP G +    + +N T +  ++D   PV
Sbjct: 290 EHI------TQPQDQKNDQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPV 343

Query: 340 KPGDKVELLADTQRLHAFDLETDRTI 365
             G+  EL+ D +++  FD ET++ I
Sbjct: 344 TWGETAELMFDMKKVVFFDPETEKRI 369


Lambda     K      H
   0.320    0.139    0.400 

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: 422
Number of extensions: 18
Number of successful extensions: 3
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: 376
Length of database: 372
Length adjustment: 30
Effective length of query: 346
Effective length of database: 342
Effective search space:   118332
Effective search space used:   118332
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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