GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Klebsiella michiganensis M5al

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 BWI76_RS06690 BWI76_RS06690 ABC transporter ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Koxy:BWI76_RS06690
          Length = 369

 Score =  346 bits (887), Expect = e-100
 Identities = 194/370 (52%), Positives = 246/370 (66%), Gaps = 29/370 (7%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           M+ +RL +V KRFG  V +   NL+ EDGEF VFVGPSGCGK+T LRMIAGLEE+SEG +
Sbjct: 1   MSNIRLRNVTKRFGSTVTLHQVNLDIEDGEFAVFVGPSGCGKSTLLRMIAGLEEVSEGEV 60

Query: 61  YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120
            IGD ++NDV P  R +AMVFQ+YALYPHM V ENM +GL++ + PKDEI R+V+  A+ 
Sbjct: 61  LIGDEVMNDVVPAHRGVAMVFQSYALYPHMTVAENMGYGLKVNKVPKDEIRRQVEMVAKT 120

Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180
           L++ HLL+RKP++LSGGQRQRVA+GRAIVR P+VF+ DEPLSNLDA+LRVEMR  IAKL 
Sbjct: 121 LQLSHLLDRKPKQLSGGQRQRVAIGRAIVRNPRVFMFDEPLSNLDAELRVEMRLHIAKLH 180

Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240
             L  T +YVTHDQVEAMTL  +IVVM  G+++Q+ +P++LY  P N+FVAGFIGSP MN
Sbjct: 181 HELKTTMVYVTHDQVEAMTLADKIVVMNYGKVEQMGSPMSLYYNPVNKFVAGFIGSPKMN 240

Query: 241 FVRAGVEV--QGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIP 298
           F+ A V     G+    +A    +  N +  S L+P  G  V LG+RPEHL     +T  
Sbjct: 241 FLPATVTAWQPGQLSVKMAQDHNLTLN-ITTSPLQP--GAAVTLGIRPEHL-----STDV 292

Query: 299 EEENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVK---PGD-------KVELL 348
               V+  + EVVE LG         N T L  +  GH  VK   PGD       K+ + 
Sbjct: 293 NIGTVVEFQCEVVERLG---------NNTYLFGQCYGHDNVKILLPGDVHFRPWQKISVA 343

Query: 349 ADTQRLHAFD 358
            D +    FD
Sbjct: 344 FDDRYCMVFD 353


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: 405
Number of extensions: 15
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: 376
Length of database: 369
Length adjustment: 30
Effective length of query: 346
Effective length of database: 339
Effective search space:   117294
Effective search space used:   117294
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