GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Shew_2731 in Pseudomonas putida KT2440

Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate PP_2797 PP_2797 acetate permease

Query= reanno::PV4:5209923
         (572 letters)



>FitnessBrowser__Putida:PP_2797
          Length = 552

 Score =  170 bits (430), Expect = 2e-46
 Identities = 148/550 (26%), Positives = 247/550 (44%), Gaps = 64/550 (11%)

Query: 1   MDVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFI 60
           +++  +   +V   F L I      R  ST +FY AGGG+    NG+A A D+MSA++ +
Sbjct: 30  LNLHAIGMFMVFVLFTLCITWWAARRTRSTTDFYSAGGGIQGWQNGLALAGDYMSASTLL 89

Query: 61  SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVA 120
            +  ++   G DG +YL+ +  G+ +L L M   LR  G+FT  D    R      RT+A
Sbjct: 90  GITALIYTSGMDGYIYLIAFFAGWPVLLLLMTERLRNLGRFTFADITSYRLDQGKVRTMA 149

Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180
            + ++ +   Y+  QM G G +      ++    V I  A++  Y   GGM   T+ Q+ 
Sbjct: 150 AIGSLTVVCFYLVAQMVGAGQLIRLLFGLDYHIAVVIVGALMMLYVTFGGMVATTWVQII 209

Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNN---TGVYLLEKLDGLSAQL 237
           +  +L+    +  +F+++         L   A    A G      G  L + L  LS  L
Sbjct: 210 KAFLLLVGGSL-VLFLAMREFDFSYDALVSKAMDTHALGERLLAPGSLLADPLTALSLSL 268

Query: 238 GFSQYTEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMY 297
           G                    L+FGTAGLPH+++RFFTV   ++AR S  +A  FI   +
Sbjct: 269 G--------------------LVFGTAGLPHILMRFFTVSDAREARKSVLYATGFIGYFF 308

Query: 298 TTIPALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKG 357
             I  L   S V + +               P + +  E  G +               G
Sbjct: 309 NVIFLLGLASIVIVSQ--------------QPKFFEGGEVGGKL--------------LG 340

Query: 358 ETNEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKK 417
             N +     +M LA     NL   ++  ++A   A  L+  +GL L  +++++HDL  +
Sbjct: 341 GGNMV-----VMHLAQAVGGNL---LLGFLSAVTFATILAVVSGLALAGASAIAHDLYAR 392

Query: 418 NFMPD-ISDKQELLYARIAA-ALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIM 475
             M    S+ QEL   ++A  +LG+V      +     VA +VA+AFG+AAS+ FP + +
Sbjct: 393 VIMKGAASEAQELRVTKLATLSLGLVAIALGILFENINVAFMVALAFGIAASANFPVLFL 452

Query: 476 GIFSRTMNKEGAIAGMVIGLLFSASYIIYFKFVNPGDNNASNWLFGISPEGIGMLGMIIN 535
            +F   +   GA+A   +GLL +  ++++ K V     + +  LF  +     +  M + 
Sbjct: 453 SMFWSGLTTRGALAAGYVGLLSAMGFVVFSKLVWVDVLHFAEPLFPYTQP--ALFSMPLA 510

Query: 536 FAVAFIVSKV 545
           F VA+ VS++
Sbjct: 511 FLVAYAVSRM 520


Lambda     K      H
   0.326    0.140    0.423 

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: 783
Number of extensions: 41
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 572
Length of database: 552
Length adjustment: 36
Effective length of query: 536
Effective length of database: 516
Effective search space:   276576
Effective search space used:   276576
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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