GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_1210 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1210
          Length = 374

 Score =  246 bits (628), Expect = 7e-70
 Identities = 147/352 (41%), Positives = 202/352 (57%), Gaps = 16/352 (4%)

Query: 14  GKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIGDRLVNDVPPK 73
           G+ + VKD NL+   GEF+  +GPSG GKTT+L M+AG E  + G I +  R +N+VPP 
Sbjct: 26  GENLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILLAGRAINNVPPH 85

Query: 74  DRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILKIEHLLNRKPRE 133
            RDI MVFQNYAL+PHM V EN+AF L +R   K ++  RVK    +++++    R P +
Sbjct: 86  KRDIGMVFQNYALFPHMTVAENLAFPLTVRGMNKSDVSARVKRVLSMVQLDAFAQRYPAQ 145

Query: 134 LSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRLGVTTIYVTHD 193
           LSGGQ+QRVA+ RA+V EP++ LMDEPL  LD +LR  M+ EI  L +RLGVT +YVTHD
Sbjct: 146 LSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQRLGVTVVYVTHD 205

Query: 194 QVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFVRAGVEVQGEKV 253
           Q EA+T+  R+ V   GEIQQ+  P  LY+ P N FVA FIG  +    R   +     +
Sbjct: 206 QGEALTMSDRVAVFHQGEIQQIAPPRTLYEEPKNTFVANFIGENNRLNGRLHSQTGDRCI 265

Query: 254 YLVAPGFRIRANAV-LGSALKPYAGKEVWLGVRPEHLGLKGYTTIPEEENVLRGEVEVVE 312
             +  G ++ A AV +G       G+ V L +RPE + L G  +  +  N   G VE   
Sbjct: 266 VELGRGEKVEALAVNVGQ-----TGEPVTLSIRPERVSLNG--SSDQCVNRFSGRVEEFI 318

Query: 313 PLGAETEIHVAVNGTL------LVAKVDGHAPVKPGDKVELLADTQRLHAFD 358
            LG    + + V G         +A++D    V  GD V L    + + A D
Sbjct: 319 YLGDHVRVRMEVCGKTDFFVKQPIAELDPSLAV--GDVVPLGWQVEHVRALD 368


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: 384
Number of extensions: 15
Number of successful extensions: 1
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: 374
Length adjustment: 30
Effective length of query: 346
Effective length of database: 344
Effective search space:   119024
Effective search space used:   119024
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