Align proline porter II (characterized)
to candidate CA265_RS19920 CA265_RS19920 MFS transporter
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__Pedo557:CA265_RS19920 Length = 507 Score = 206 bits (525), Expect = 1e-57 Identities = 142/492 (28%), Positives = 238/492 (48%), Gaps = 91/492 (18%) Query: 25 KAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGGL 84 K I A+SLG +EW+DF ++G +A +G FP + ++ LA F+ F++RP G L Sbjct: 12 KVIGASSLGTLIEWYDFYIFGSLAVIIGHQLFPEDAGASALINTLAIFAAGFIVRPFGAL 71 Query: 85 FFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGGE 144 FG LGD GR+ +T+V+M STF IGLIPSY +IG APIL+LI ++ QG ++GGE Sbjct: 72 VFGRLGDLIGRKYTFLLTLVLMGGSTFFIGLIPSYKSIGYAAPILVLILRLIQGLALGGE 131 Query: 145 YTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIPF 204 Y GA+ +VAE++P KRGF SW+ + G L G++V+ I+G F DWGWRIPF Sbjct: 132 YGGAATYVAEHAPKNKRGFFTSWIQTTATLGLFLSLGIIVITKNILGAETFGDWGWRIPF 191 Query: 205 FIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLTC 264 +++ L ++ +Y+R + E+P F + + + ++ K SF A + LL Sbjct: 192 LLSIVLVVVSIYIRMKMHESPMFSKL-----KAEGNVSKNPLKESFNNKAN-FKMVLLAL 245 Query: 265 IGLVIATNVTYYMLLTYMPSYLSHN--LHYSEDHGVLI---------------------- 300 G + V +Y Y S+L + L +++ +L+ Sbjct: 246 FGATMGQGVIWYTGQFYAQSFLENTCKLDFNDSRYILLWGIAFATPFFVIFGAWSDKVGR 305 Query: 301 ----IIAIMIGMLFVQPVMGLL-----------SDRFGRRPF------------------ 327 + +++G+LF +P+ + +D RP Sbjct: 306 KWIMLSGMLLGILFYRPIYQIFLDDTDYTKIEQTDILSARPAPVTSVLIANSTDSLRTVS 365 Query: 328 --VLLGSVALF------VLAIPAFILINSNVI--------------GLIFAGLLMLAVIL 365 V+L + A F ++ IL+ V+ GLIF +L++ ++ Sbjct: 366 TKVMLKNGASFNKVQTDTVSATKGILLGKEVVKDKILPTPVFWKFVGLIFFQILLVTMVY 425 Query: 366 NCFTGVMASTLPAMFPTHIRYSALAAAFNI-SVLVAGLTPTLAAWLVE-SSQNLMMPAYY 423 G +A+ L +FPT IRY++++ ++I + + GL P +A + S + +Y Sbjct: 426 ----GPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPFIATLIASFSGSTPLSGLWY 481 Query: 424 LMVVAVVGLITG 435 + +A + L+ G Sbjct: 482 PIGIAALSLVIG 493 Lambda K H 0.327 0.142 0.429 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: 698 Number of extensions: 40 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 500 Length of database: 507 Length adjustment: 34 Effective length of query: 466 Effective length of database: 473 Effective search space: 220418 Effective search space used: 220418 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 (21.7 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