Alignments for a candidate for actP in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Pseudomonas putida KT2440

Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate PP_2797 PP_2797 acetate permease

Query= SwissProt::P32705
         (549 letters)



>FitnessBrowser__Putida:PP_2797
          Length = 552

 Score =  635 bits (1638), Expect = 0.0
 Identities = 318/549 (57%), Positives = 407/549 (74%), Gaps = 4/549 (0%)

Query: 5   LTALAATLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSRSDYY 64
           L  LA  L      A     A +RQP N  AI MF++FV+FTL IT+WA++R RS +D+Y
Sbjct: 4   LVPLALLLHSGLLLASPSLDAGQRQPLNLHAIGMFMVFVLFTLCITWWAARRTRSTTDFY 63

Query: 65  TAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFLIAER 124
           +AGG I G+QNGLA+AGDYMSA++ LGI+AL++TSG DG IY + F  GWP++L L+ ER
Sbjct: 64  SAGGGIQGWQNGLALAGDYMSASTLLGITALIYTSGMDGYIYLIAFFAGWPVLLLLMTER 123

Query: 125 LRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLNYHIA 184
           LRNLGR+TFAD+ SYRL QG +R ++A GSL VV  YL+AQMVGAG+LI LLFGL+YHIA
Sbjct: 124 LRNLGRFTFADITSYRLDQGKVRTMAAIGSLTVVCFYLVAQMVGAGQLIRLLFGLDYHIA 183

Query: 185 VVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSEAMAV 244
           VV+VG LMM+YV FGGM+ATTWVQIIKA LLL G S + F+ M+   FS++ L S+AM  
Sbjct: 184 VVIVGALMMLYVTFGGMVATTWVQIIKAFLLLVGGSLVLFLAMREFDFSYDALVSKAMDT 243

Query: 245 HPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVFYATGF 304
           H  G  ++ PG L+ DP++ALSL LGL+FGTAGLPHILMRFFTVSDAREARKSV YATGF
Sbjct: 244 HALGERLLAPGSLLADPLTALSLSLGLVFGTAGLPHILMRFFTVSDAREARKSVLYATGF 303

Query: 305 MGYFYILTFIIGFGAIMLVGANPEY---KDAAGHLIGGNNMAAVHLANAVGGNLFLGFIS 361
           +GYF+ + F++G  +I++V   P++    +  G L+GG NM  +HLA AVGGNL LGF+S
Sbjct: 304 IGYFFNVIFLLGLASIVIVSQQPKFFEGGEVGGKLLGGGNMVVMHLAQAVGGNLLLGFLS 363

Query: 362 AVAFATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKITVLILGVIAIILG 420
           AV FATILAVV+GL LAGASA++HDLYA V  KG A+E +ELRV+K+  L LG++AI LG
Sbjct: 364 AVTFATILAVVSGLALAGASAIAHDLYARVIMKGAASEAQELRVTKLATLSLGLVAIALG 423

Query: 421 VLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMILGP 480
           +LFEN N+AFMV LAF IAAS NFP++ LSM+WS LTTRGA+  G++GL++A+  ++   
Sbjct: 424 ILFENINVAFMVALAFGIAASANFPVLFLSMFWSGLTTRGALAAGYVGLLSAMGFVVFSK 483

Query: 481 TIWVQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFIRSQTG 540
            +WV +L   + +FPY  PALFS+ +AFL  +  S  D +A    ER  F  QF+R QTG
Sbjct: 484 LVWVDVLHFAEPLFPYTQPALFSMPLAFLVAYAVSRMDRTARAKAERAAFADQFVRGQTG 543

Query: 541 FGVEQGRAH 549
            G      H
Sbjct: 544 LGASGAVDH 552


Lambda     K      H
   0.329    0.142    0.424 

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: 906
Number of extensions: 51
Number of successful extensions: 5
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: 549
Length of database: 552
Length adjustment: 36
Effective length of query: 513
Effective length of database: 516
Effective search space:   264708
Effective search space used:   264708
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: 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources