GapMind for catabolism of small carbon sources

 

Alignments for a candidate for actP in Pseudomonas stutzeri RCH2

Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate GFF2882 Psest_2938 transporter, SSS family

Query= SwissProt::P32705
         (549 letters)



>FitnessBrowser__psRCH2:GFF2882
          Length = 551

 Score =  808 bits (2087), Expect = 0.0
 Identities = 406/550 (73%), Positives = 471/550 (85%), Gaps = 2/550 (0%)

Query: 1   MKRVLTALAATLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSR 60
           ++ ++TAL   +   A  ADAI+G VE+Q TN+ AIIMF++F+ FT+GIT WA+KR  S 
Sbjct: 3   LRFLMTALLLAVS-PALLADAITGEVEKQATNYTAIIMFVVFIAFTMGITKWAAKRNTST 61

Query: 61  SDYYTAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFL 120
           +DYYTAGG+ITGFQNGLAIAGD+MSAASFLGISALV+TSGYDGLIYS+GFLVGWPIILFL
Sbjct: 62  ADYYTAGGSITGFQNGLAIAGDFMSAASFLGISALVYTSGYDGLIYSIGFLVGWPIILFL 121

Query: 121 IAERLRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLN 180
           +AERLRNLG++TF+DVASYRL Q  IR+LSA GSL+VVA YLIAQMVGAGKLI+LLFGL+
Sbjct: 122 MAERLRNLGKFTFSDVASYRLGQTQIRLLSAFGSLIVVAFYLIAQMVGAGKLIQLLFGLD 181

Query: 181 YHIAVVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSE 240
           Y++AVVLVGVLM+MYVLFGGMLATTWVQIIKAVLLL GASFMA MVMK VGF F +LF+E
Sbjct: 182 YYVAVVLVGVLMVMYVLFGGMLATTWVQIIKAVLLLSGASFMAIMVMKSVGFDFGSLFAE 241

Query: 241 AMAVHPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVFY 300
           A+ +H KG  IM PGGLV DPISA+SLGL LMFGTAGLPHILMRFFTVSDA+EARKSVFY
Sbjct: 242 AVKIHEKGAQIMSPGGLVSDPISAISLGLALMFGTAGLPHILMRFFTVSDAKEARKSVFY 301

Query: 301 ATGFMGYFYILTFIIGFGAIMLVGANPEYKDAAGHLIGGNNMAAVHLANAVGGNLFLGFI 360
           ATGF+GYFYILTFIIGFGAI+LV  NPE+KD  G ++GG NM A+HLA+AVGGNLFLGFI
Sbjct: 302 ATGFIGYFYILTFIIGFGAILLVSTNPEFKDVTGAIVGGTNMVAIHLASAVGGNLFLGFI 361

Query: 361 SAVAFATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKITVLILGVIAIIL 419
           SAVAFATILAVVAGLTLAGASAVSHDLYA V K+G A E +E+RV+K+T L LGV+AI+L
Sbjct: 362 SAVAFATILAVVAGLTLAGASAVSHDLYACVIKQGKAREEDEMRVTKLTTLTLGVVAILL 421

Query: 420 GVLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMILG 479
           G++FE QNIAFMVGLAF+IAASCNFP++ LSMYW  L+TRGA+ GG LGL TA++L I+ 
Sbjct: 422 GIIFEKQNIAFMVGLAFSIAASCNFPVLFLSMYWKGLSTRGALFGGSLGLFTALLLTIIS 481

Query: 480 PTIWVQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFIRSQT 539
           PT+WV + G  +AIFPY+YPALFS+  AF GIWFFS TD S     ERE F AQF+RSQT
Sbjct: 482 PTVWVDVFGFAEAIFPYKYPALFSMAAAFAGIWFFSVTDKSKRAGEERERFFAQFVRSQT 541

Query: 540 GFGVEQGRAH 549
           G G     AH
Sbjct: 542 GLGATGAVAH 551


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: 1028
Number of extensions: 39
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: 549
Length of database: 551
Length adjustment: 36
Effective length of query: 513
Effective length of database: 515
Effective search space:   264195
Effective search space used:   264195
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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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