Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate RR42_RS33495 RR42_RS33495 aromatic amino acid transporter
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__Cup4G11:RR42_RS33495 Length = 465 Score = 632 bits (1630), Expect = 0.0 Identities = 301/446 (67%), Positives = 366/446 (82%) Query: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEMV 69 LKRGLKNRHIQLIALGGAIGTGLFLG A ++ AGPS++LGYA+ G+IAF IMRQLGEMV Sbjct: 13 LKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLGEMV 72 Query: 70 AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWVS 129 EPVAGSFSHFA KY G F GF+SGWNYWVLY+LVSMAEL+AVG YV YWWP +PTW S Sbjct: 73 VDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPTWAS 132 Query: 130 ALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQASISNLW 189 AL F INAINL +VK++GE EFWF+I+KV+A++GMI+FGGYLL SG GPQAS+SNLW Sbjct: 133 ALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASGTAGPQASVSNLW 192 Query: 190 SHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRILIFYI 249 HGGFFP+G GL +AVIMFSFGGLEL+GITAAEADEP+K+IPKA NQVIYRILIFY+ Sbjct: 193 QHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQVIYRILIFYV 252 Query: 250 CSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNSGVYANSRM 309 +L VLLSLYPW +V GGSPFV+IF + S + A VLN VVLTAALSVYNSGVY NSRM Sbjct: 253 GALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYNSGVYCNSRM 312 Query: 310 LYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLLMALVVAAL 369 L+GLA+QGNAP+AL+KV++RG+P A+G+SALAT CV++NY +P EA LLM LVV+AL Sbjct: 313 LFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEAFELLMGLVVSAL 372 Query: 370 VLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILAMTPGLSVSV 429 ++NWA+IS+ HLK RR AAG+ FKS +P++N++CLAF+A IL ++ +TPGL +SV Sbjct: 373 IINWAMISIIHLKFRRDKRAAGQETRFKSLGYPLTNYVCLAFLAGILYVMYLTPGLRISV 432 Query: 430 LLVPLWLVVMWAGYAFKRRRAAAHVA 455 L+P WL V+ Y ++++ A A Sbjct: 433 YLIPAWLAVLGLSYRLRQKQKRAEPA 458 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: 617 Number of extensions: 15 Number of successful extensions: 1 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: 465 Length adjustment: 33 Effective length of query: 428 Effective length of database: 432 Effective search space: 184896 Effective search space used: 184896 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