Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate PfGW456L13_4400 Aromatic amino acid transport protein AroP
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4400 Length = 473 Score = 613 bits (1580), Expect = e-180 Identities = 302/464 (65%), Positives = 363/464 (78%), Gaps = 10/464 (2%) Query: 6 QQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQL 65 Q LKRGLKNRHIQLIALGGAIGTGLFLGSA VL++AGPSMILGYAI G IAFMIMRQL Sbjct: 7 QSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQL 66 Query: 66 GEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVP 125 GEM+ ++PVAGSFSHFA+KYWG F GFLSGWN W+LY+LV M+ELTAVG Y+HYW P +P Sbjct: 67 GEMIVEDPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIP 126 Query: 126 TWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQASI 185 TW SA F INAINLANVK +GE EFWFAIIKVVA++GMI G YLLVSG+GGPQA++ Sbjct: 127 TWASAAAFFVLINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGNGGPQAAV 186 Query: 186 SNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRIL 245 SNLWSHGGFFP+G GL +A IMFSFGGLE++G TAAEAD+P+ IPKA+NQVIYRIL Sbjct: 187 SNLWSHGGFFPNGVTGLVMAMAFIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIYRIL 246 Query: 246 IFYICSLAVLLSLYPWNEV-----AAG----GSPFVMIFSQIGSTLTANVLNVVVLTAAL 296 IFYI +L +LLSL PW+ + A+G GSPFV +FS +GS A++LN VVLTAAL Sbjct: 247 IFYIGALVILLSLTPWDSLLTTLNASGDSYSGSPFVQVFSMLGSNTAAHILNFVVLTAAL 306 Query: 297 SVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAE 356 SVYNSG Y NSRML G+AEQG+AP+AL K+D+RGVP +I SA T V++NYLIP Sbjct: 307 SVYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAVTLIAVLLNYLIPHS 366 Query: 357 ALGLLMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALIL 416 AL LLM+LVVA LV+NWA+IS +H K R+ M +T +FK+ W+P N+ICLAF+ IL Sbjct: 367 ALELLMSLVVATLVINWAMISYSHFKFRQHMNKTKQTPLFKALWYPYGNYICLAFVLFIL 426 Query: 417 VILAMTPGLSVSVLLVPLWLVVMWAGYAFKRRRAAAHVAARVVG 460 ++ + PG+ SV +P+WLV MW Y K +R+A H A +V G Sbjct: 427 GVMLLIPGIQTSVYAIPVWLVFMWVCYGIKNKRSAQH-ALQVAG 469 Lambda K H 0.327 0.140 0.440 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: 655 Number of extensions: 23 Number of successful extensions: 3 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: 461 Length of database: 473 Length adjustment: 33 Effective length of query: 428 Effective length of database: 440 Effective search space: 188320 Effective search space used: 188320 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: 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:
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