Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate BPHYT_RS25605 BPHYT_RS25605 symporter
Query= SwissProt::P32705 (549 letters) >lcl|FitnessBrowser__BFirm:BPHYT_RS25605 BPHYT_RS25605 symporter 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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