GapMind for catabolism of small carbon sources

 

Aligments for a candidate for thuG in Dinoroseobacter shibae DFL-12

Align Maltose transport system permease protein malG aka TT_C1629, 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 3609759 Dshi_3142 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= TCDB::Q72H66
         (280 letters)



>lcl|FitnessBrowser__Dino:3609759 Dshi_3142
           binding-protein-dependent transport systems inner
           membrane component (RefSeq)
          Length = 275

 Score =  171 bits (432), Expect = 2e-47
 Identities = 90/266 (33%), Positives = 151/266 (56%), Gaps = 7/266 (2%)

Query: 15  LLVVFVVVYSVFPFYWAVISSFKPSDALFSPDPSFLPVPFTLEHYENVFLQA-NFGRNLL 73
           +L++  +   + P  W  +++FK    ++     F P   TLE++  VF      G  L 
Sbjct: 16  VLIIAAMFVMLVPILWIFLAAFKSHVDVYQLKLFFTP---TLENFGTVFDDPYRLGEKLF 72

Query: 74  NSLIVAGGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAVLGGLFLLLRQ 133
           NS +VA    ++++ +  LAAY+  R     + A++ ++L+    P + ++   F++ R 
Sbjct: 73  NSTVVALVTVVIAIPIATLAAYSFSRFRLVGETAMLVVILATQFLPAVVIILPFFIMFRD 132

Query: 134 TGLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQTLLKVMLPLT 193
            GL +T LGLIL  L   +PF +W++ G+  G+P + EEAA VDG++ LQ +  ++LP+ 
Sbjct: 133 IGLLDTRLGLILVNLAIVMPFAIWMIKGFIDGIPLDTEEAAMVDGSSRLQVIWNIVLPMA 192

Query: 194 GPGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGATPFEIPWGSIMAASVV 253
            PGL+T+G+  FI AWNE+LFAL  T  D+V T+P  +A F G       W  + AA ++
Sbjct: 193 APGLLTSGIFCFIIAWNEFLFALILTNKDAV-TLPIGLALFKGEE--GDLWNLLSAAGII 249

Query: 254 VTVPLVVLVLVFQQRIVAGLTAGAVK 279
           +  P+ VL L+ ++  V G+T GAV+
Sbjct: 250 IMAPMFVLALMIRKYFVQGMTMGAVR 275


Lambda     K      H
   0.329    0.145    0.439 

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: 137
Number of extensions: 10
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: 280
Length of database: 275
Length adjustment: 25
Effective length of query: 255
Effective length of database: 250
Effective search space:    63750
Effective search space used:    63750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 47 (22.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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