Align Phenylacetate permease, Ppa (characterized)
to candidate BPHYT_RS11800 BPHYT_RS11800 acetate permease
Query= TCDB::O50471 (520 letters) >FitnessBrowser__BFirm:BPHYT_RS11800 Length = 528 Score = 397 bits (1021), Expect = e-115 Identities = 215/527 (40%), Positives = 325/527 (61%), Gaps = 22/527 (4%) Query: 6 ISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFLGISAM 65 I F+ F+ +L++T W+A R+R S F+ AG L+ QNGLA+AGD +SA SFLG++ + Sbjct: 12 IIAFVGFIGLSLVLTGWSARRSRGTSGFFVAGRNLSPFQNGLALAGDFMSAGSFLGVTGL 71 Query: 66 MFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTSAFGTL 125 + + G+DG++Y +G +AGW +I+ ++AE +RN GKYT +DVV+ RL VR ++ +L Sbjct: 72 VSLFGFDGIVYQVGFIAGWIMIMLIVAEPVRNCGKYTLSDVVALRLRSRGVRAATSVSSL 131 Query: 126 VVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQIIKAVML 185 + +L YL+AQ+VG G L LL I A++L+G+LM+AYV FGGM+A T+VQI+KAV++ Sbjct: 132 ITSLAYLLAQLVGGGALASLLLPIGTNAAIVLIGILMIAYVLFGGMVAATYVQIVKAVLV 191 Query: 186 LSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLGMMFGT 245 + + + + L HF F A+F A PGG +P+D +SL L + GT Sbjct: 192 WTAGAVLVLLALAHFSFDVGALFNKARLSSLHPAQYFVPGGYFKDPLDTLSLTLALALGT 251 Query: 246 AGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVG------TEPSY 299 AGLPH++ RF+TV A ARKS + F +++I++GF A +VG T S Sbjct: 252 AGLPHVMTRFYTVPSAVAARKSAKIGLIVMTSFAVMMILLGFSATAIVGPAAILATHSSG 311 Query: 300 RDA---TGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHD 356 A +GGG A + GG L L +SA+AFATILAVV+G+ +S AS +SHD Sbjct: 312 NSAITLLATTLGGG-------AGSAGGELLLACVSAIAFATILAVVSGIMISSASTISHD 364 Query: 357 LYACVIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFP 416 ++ + + E+ ++ +++IAT++ G+ A+ L L+ ++ N+AFL GL A+AAS N P Sbjct: 365 IFGQLFSASRDKERRQVVIAKIATIVFGIAAMGLALLVKTFNVAFLVGLAFAIAASANLP 424 Query: 417 VLLLSMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVN---VLHHEKALFPYSNPALF 473 V+L SM+W+ T RGAV +AG S++ LV+LGPAV + F SNP LF Sbjct: 425 VILFSMYWRRFTDRGAVAAVLAGTLSSIGLVLLGPAVIGAKGIIFKDSTPPFWLSNPGLF 484 Query: 474 SMSLAFLSAWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520 S+ + F++ W+ SVT S A + AQ +R ++G+GA AS+H Sbjct: 485 SIPVGFIAGWIGSVTTSQNAADTS---FDAQQLRMLSGLGAEAASEH 528 Lambda K H 0.328 0.139 0.407 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: 750 Number of extensions: 49 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: 520 Length of database: 528 Length adjustment: 35 Effective length of query: 485 Effective length of database: 493 Effective search space: 239105 Effective search space used: 239105 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: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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