Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate BPHYT_RS25605 BPHYT_RS25605 symporter
Query= SwissProt::P32705 (549 letters) >FitnessBrowser__BFirm:BPHYT_RS25605 Length = 516 Score = 400 bits (1028), Expect = e-116 Identities = 222/513 (43%), Positives = 325/513 (63%), Gaps = 22/513 (4%) Query: 36 IIMFLIFVVFTLGITYWASKRVRSRSDYYTAGGNITGFQNGLAIAGDYMSAASFLGISAL 95 I++F+I + TL ITYWA++R R+ S++Y AGGN++ +NG A+AGD+MSAA+FLG S L Sbjct: 6 IVIFMIILAVTLMITYWAARRTRTTSEFYAAGGNLSARENGFALAGDWMSAAAFLGFSGL 65 Query: 96 VFTSGYDGLIYSLGFLVGWPIILFLIAERLRNLGRYTFADVASYRLKQGPIRILSACGSL 155 V G DG +Y++ L + ++L LIAE +RN GRYTF DV + R+K+ R+ + G++ Sbjct: 66 VSLYGMDGSLYAVAALAAFLVVLMLIAEPVRNTGRYTFGDVIAERMKRPGARLATIVGTV 125 Query: 156 VVVALYLIAQMVGAGKLIELLFGLNYHIAVVLVGVLMMMYVLFGGMLATTWVQIIKAVLL 215 VV Y++ QM GAG LI+L+ G+ Y +AVVLVG+ M++YVLFGGM+ATTWVQI+KA+LL Sbjct: 126 VVNLAYMVPQMAGAGALIKLMLGVPYDVAVVLVGIGMIVYVLFGGMIATTWVQIVKAMLL 185 Query: 216 LFGASFMAFMVMKHVGFSFNNLFSEAMAVHPKGVDIMKPGGLVKDPISALSLGLGLMFGT 275 L A + M++ V F+ LF+ ++ G ++ GG P+ +SL + +FG Sbjct: 186 LVAACVLVSMLLAAVRFNPLALFASVERLY--GSKMLASGGYFHHPLDTMSLFISFIFGV 243 Query: 276 AGLPHILMRFFTVSDAREARKSVFYATGFMGYFYILTFIIGFGAIMLVGANPEYKDAAGH 335 AGLPHI+ RF+TV DAR ARKSV + G F+++T +IGF + + VG +DA Sbjct: 244 AGLPHIMTRFYTVPDARTARKSVLWLMFLAGSFFMVTTLIGFASAVFVG-----QDAIRA 298 Query: 336 LIGGNNMAAVHL-------ANAVGGNLFLGFISAVAFATILAVVAGLTLAGASAVSHDLY 388 G N+A L A ++GG +FL I A+AFA ILAVVAGLTLA + A++HDLY Sbjct: 299 ADKGGNLALPLLAQYLGGGAGSLGGQIFLASICAIAFAAILAVVAGLTLASSGAIAHDLY 358 Query: 389 ANVFKKGA-TEREELRVSKITVLILGVIAIILGVLFENQNIAFMVGLAFAIAASCNFPII 447 NV +KGA ++ E++RV++I + +G+ AI L +L + N+ +V LA ++AAS NFPII Sbjct: 359 VNVLRKGAVSDAEQVRVARIATVAVGIAAIGLSLLAQGLNVGVLVILAISVAASSNFPII 418 Query: 448 LLSMYWSKLTTRGAMMGGWLGLITAVVLMILGPTIWVQILGHEKAIFPYEYPALFSITVA 507 LLS++W + T G + G GL ++V L +GP A+FP PA+ S+ + Sbjct: 419 LLSIFWRRFNTAGVIGGVIGGLTSSVALAFVGPAFM-----GSHALFPIVNPAIVSLPIG 473 Query: 508 FLGIWFFSATDNSAEGARERELFRAQFIRSQTG 540 W T S + F A ++R+QTG Sbjct: 474 LFSAWL--CTMLSRPTPTQDGDFEAFYLRAQTG 504 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: 733 Number of extensions: 45 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: 516 Length adjustment: 35 Effective length of query: 514 Effective length of database: 481 Effective search space: 247234 Effective search space used: 247234 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