GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Desulfovibrio vulgaris Miyazaki F

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 8500849 DvMF_1587 ABC transporter related (RefSeq)

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Miya:8500849
          Length = 366

 Score =  214 bits (545), Expect = 3e-60
 Identities = 142/380 (37%), Positives = 199/380 (52%), Gaps = 43/380 (11%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           MA + L  + K +G    +   +L    GE    +GPSGCGKT  LR+IAG E    G I
Sbjct: 1   MADITLAGIGKAYGAHAVLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAGTI 60

Query: 61  YIGDRLVND------VPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRV 114
            IG   V+D      VPP  RD+ +VFQ+YA++PHM+V +N+ + L+L   P  E  R+V
Sbjct: 61  SIGGEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTRQV 120

Query: 115 KEAARILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRA 174
            E   ++ +  L NR P +LSGGQ+QRVA+ RA+V  P + L+DEPL NLDA LR EMR 
Sbjct: 121 LETVEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEMRF 180

Query: 175 EIAKLQRRLGVTTIYVTHDQVEAMTLGHRIVVMKD-GEIQQVDTPLNLYDFPANRFVAGF 233
           EI +LQR LG+T +YVTHDQ  A+ +  R+ +M   G I+QV TP  +++ PA+ FV  F
Sbjct: 181 EIKELQRTLGITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVFRF 240

Query: 234 IGSPSMNFVRAGVEVQGEKVYLVAPGFRIRANAVLGSALK-------PYAGKEVWL-GVR 285
           +G    NF+ A                R R  A+L +  +       P    E W+ G R
Sbjct: 241 MG--VANFLPA----------------RRRGMAMLAAGGEQPVPWGLPDGDAEHWMAGFR 282

Query: 286 PEHLGLKGYTTIPEEENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPG--- 342
           P  + L        + + LRG V     LGA T+  + V+G     ++D H  +  G   
Sbjct: 283 PSDVRL------ARQGDGLRGTVRRASFLGAMTDYLIEVDGASFRTQLDTHEALARGLMF 336

Query: 343 -DKVELLADTQRLHAFDLET 361
            +    +     LH FD  T
Sbjct: 337 AEGEPCVVGFHDLHWFDAAT 356


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: 324
Number of extensions: 11
Number of successful extensions: 4
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: 366
Length adjustment: 30
Effective length of query: 346
Effective length of database: 336
Effective search space:   116256
Effective search space used:   116256
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: 49 (23.5 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