GapMind for catabolism of small carbon sources

 

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

Align Glycine betaine/proline/choline transporter VP1723 (characterized)
to candidate PfGW456L13_1085 High-affinity choline uptake protein BetT

Query= SwissProt::Q87NZ5
         (553 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1085
          Length = 665

 Score =  341 bits (874), Expect = 6e-98
 Identities = 179/527 (33%), Positives = 295/527 (55%), Gaps = 32/527 (6%)

Query: 32  LKVGPFGLDIHNRVFAISGMAIVLFVVATLTFRQQVEPFFAGLRAWLVSNLDWFFLASGN 91
           +K  P  + ++  VF  S   I+L     +   Q+        +AWL  +  W+++    
Sbjct: 7   IKTPPEKVTVNGWVFYTSTALILLLTAILIIAPQEAGRMLGTAQAWLSRSFGWYYMVVIA 66

Query: 92  VFVIVCLVLIVTPLGRVRIGGTEATPDYSYAGWLAMLFAAGMGIGLVFFGVSEPMSHFSS 151
            ++I  + L  +  G++++G  + TPD+SY  W  MLF++G+GI L++FG SEP+ H+ +
Sbjct: 67  AYLIFVVGLAFSSYGKLKLGSKDDTPDFSYGAWAGMLFSSGIGISLLYFGASEPLDHYFN 126

Query: 152 ALGGVNIENGVRTDWAPLGGAVGDTDAASALGMAATIYHWALHPWSIYALLALGLAIFSF 211
              GV                   ++ A+   +  T  HW LH W+IYAL+ L +A F++
Sbjct: 127 PPEGV-----------------AGSNLAARQAVQLTFLHWGLHGWAIYALVGLAVAYFAY 169

Query: 212 NKGLPLTMRSIFYPLFGER-VWGWVGHIIDILAVVATVFGLATSLGYGASQAATGLNFLF 270
               PL +RS  YPL GER V G  GH +D   +  T+ GL T+LG G+ Q ++GL  LF
Sbjct: 170 RHNQPLALRSALYPLVGERWVKGAAGHAVDGFGMFVTLLGLVTNLGIGSLQVSSGLENLF 229

Query: 271 GVPMTDTTQVVLIVVITALALISVVAGLDSGVKRLSEINMILAAMLLFFVIIVGPTMAIL 330
           G+  ++T  +++I+V++ +A I+ V+G+++G++RLS +N++L + LL FV++ GPT+ +L
Sbjct: 230 GMEHSNTNLLIVIIVMSTVATIAAVSGVENGIRRLSNLNIVLFSGLLIFVLLFGPTLHLL 289

Query: 331 TGFFDNIASYITNIPALSMPF-------EREDVNYSQGWTAFYWAWWISWSPFVGMFIAR 383
            GF  N+  Y+  +   +          E+ D  +   WT FYWAWWISW+PFVGMFIAR
Sbjct: 290 NGFVQNVGDYLNGVVLKTFDLYVYEGDSEKSD-RWLGLWTLFYWAWWISWAPFVGMFIAR 348

Query: 384 VSRGRSVREFIICVILIPSTVCVLWMTAFGGTAISQYVNDGYEAVFNAEL---PLKLFAM 440
           +SRGR+VRE +  V+LIP    + W++ FG +A+   +N G   +    L    + ++ +
Sbjct: 349 ISRGRTVRELVAGVLLIPLGFTLAWLSIFGNSALDLVMNHGAVELGKTALEQPSMAIYQL 408

Query: 441 LDVMPFAEITSVVGIILVVVFFITSSDSGSLVIDTIAA-GGKVDAPTPQ--RVFWCTFEG 497
           L+  P +++   V I +  V F+T +DSG++++  ++  GG VD   P   R+FW     
Sbjct: 409 LEHYPASKVVIGVSIFVGFVLFLTPADSGAVMMANLSCKGGNVDEDAPHWLRIFWSAVIT 468

Query: 498 LVAIALMLGGGLAAAQAMAVTTGLPFTIVLLVATVSLIKGLMDEPRL 544
           LV I L+  G   A Q M V  GLPF++VL+     L K +  + ++
Sbjct: 469 LVTIGLLFAGNFEAMQTMVVLAGLPFSVVLVFFMFGLHKAMRQDVQI 515


Lambda     K      H
   0.327    0.141    0.435 

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: 916
Number of extensions: 56
Number of successful extensions: 6
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: 553
Length of database: 665
Length adjustment: 37
Effective length of query: 516
Effective length of database: 628
Effective search space:   324048
Effective search space used:   324048
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 (21.7 bits)
S2: 53 (25.0 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