GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Herbaspirillum seropedicae SmR1

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 HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__HerbieS:HSERO_RS16715
          Length = 361

 Score =  356 bits (914), Expect = e-103
 Identities = 198/372 (53%), Positives = 252/372 (67%), Gaps = 21/372 (5%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           MA V++  V K+FG    ++  +++  DGEF V VGPSGCGK+T LRM+AGLEEI+ G I
Sbjct: 1   MASVQIRAVKKQFGSTQIIRGVDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGGEI 60

Query: 61  YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120
            IG  +VN+V PKDRDIAMVFQNYALYPHM V +NMAF L L +  K  +D RVK+AA I
Sbjct: 61  LIGGTVVNNVQPKDRDIAMVFQNYALYPHMTVRDNMAFSLTLAKKDKAFVDERVKKAADI 120

Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180
           L +  LL+R PR+LSGGQRQRVAMGRAIVR+P+VFL DEPLSNLDAKLRV+MR EI +L 
Sbjct: 121 LGLNQLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKELH 180

Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240
           +RL  T+IYVTHDQ+EAMT+  +IVVM+DG ++Q   PL+LYD+PAN FVAGFIGSP+MN
Sbjct: 181 QRLKTTSIYVTHDQIEAMTMADQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPAMN 240

Query: 241 FVRA-------GVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKG 293
           F+ A       G EV+       A G R+   A  G+AL+   G++V  GVRPEHL    
Sbjct: 241 FIPATLRRNATGAEVE------FADGTRV--PAPYGAALQGNDGQKVTYGVRPEHL---- 288

Query: 294 YTTIPEEENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLADTQR 353
             +I      +  +V VVEP GA+TE+      T L +          GD + L+ D  R
Sbjct: 289 --SIGAAGQGIATKVIVVEPTGADTEVFSRFGDTSLTSIFRERHDFGAGDVIHLVPDHSR 346

Query: 354 LHAFDLETDRTI 365
            H FD E+ +++
Sbjct: 347 THLFDAESGKSL 358


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: 409
Number of extensions: 17
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: 361
Length adjustment: 30
Effective length of query: 346
Effective length of database: 331
Effective search space:   114526
Effective search space used:   114526
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