Align Amino-acid permease RocE (characterized)
to candidate Pf6N2E2_5633 Aromatic amino acid transport protein AroP
Query= SwissProt::P39137 (467 letters) >lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5633 Aromatic amino acid transport protein AroP Length = 472 Score = 278 bits (711), Expect = 3e-79 Identities = 160/477 (33%), Positives = 255/477 (53%), Gaps = 24/477 (5%) Query: 1 MNTNQDNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIM 60 M+ + +L+R +K+RH+ +I+LGG IGTG FLG+ + AGP +L Y + GFI Sbjct: 1 MSGQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGP-SMILGYAICGFIA 59 Query: 61 FLTMLCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQ 120 F+ M LGE+ V PV+GSF +A K+ GF GW W+ + + E + G+ + Sbjct: 60 FMIMRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIH 119 Query: 121 RWFPHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLI 180 W P I W+ F L+ ++N K F E+EFWF+ IK++ I+ I LG + L+ Sbjct: 120 YWAPDIPTWVSAAAFFILINVINLANVKVFGEAEFWFAIIKVVAIVGMIALGS---YLLV 176 Query: 181 DLKGGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPR 240 GG QA + G FPNG+ +++ M + F+F G E++G A E++ P+ IP+ Sbjct: 177 SGHGGPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPK 236 Query: 241 SIKQTVWRTLVFFVLSIIVIAGMIPWKQA---------GVVESPFVAVFEQIGIPYAADI 291 +I Q ++R L+F++ +++V+ + PW SPFV VF +G AA I Sbjct: 237 AINQVIYRILIFYIGALVVLLSLTPWDSLLSTLNASGDAYSGSPFVQVFSMLGSNTAAHI 296 Query: 292 MNFVILIALLSVANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLS 351 +NFV+L A LSV NSG Y ++R+L MA +G A K L K ++RGVP+ S++ + AV ++ Sbjct: 297 LNFVVLTAALSVYNSGTYCNSRMLLGMAEQGDAPKVLSKIDKRGVPVRSILASAAVTLVA 356 Query: 352 LLTKFAQAETVYMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPV 411 +L + + +L+SL + + W IS S FR+ + + FK YP Sbjct: 357 VLLNYLIPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTH---QTPLFKALWYPY 413 Query: 412 LPLIGLTLNTVVLISLAFDPEQRIALYC---GVPFMIICYIIYHVVIKKRQQANRQL 465 I L +L + P ++++Y V FM +CY IK ++ A ++L Sbjct: 414 GNYICLAFVVFILGVMLLIPGIQVSVYAIPVWVVFMAVCY-----WIKNKRSARQEL 465 Lambda K H 0.329 0.142 0.438 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: 534 Number of extensions: 35 Number of successful extensions: 4 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: 467 Length of database: 472 Length adjustment: 33 Effective length of query: 434 Effective length of database: 439 Effective search space: 190526 Effective search space used: 190526 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: 51 (24.3 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