Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate GFF4342 PS417_22235 aromatic amino acid transporter
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__WCS417:GFF4342 Length = 473 Score = 619 bits (1595), Expect = 0.0 Identities = 301/456 (66%), Positives = 357/456 (78%), Gaps = 9/456 (1%) Query: 10 LKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQLGEMV 69 LKRGLKNRHIQLIALGGAIGTGLFLGSA VL++AGPSMILGYAI G IAFMIMRQLGEM+ Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEMI 70 Query: 70 AQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGVPTWVS 129 +EPVAGSFSHFA+KYWG F GFLSGWN W+LY+LV M+ELTAVG YVHYWWP +PTWVS Sbjct: 71 VEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYVHYWWPEIPTWVS 130 Query: 130 ALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQASISNLW 189 A F IN INLANVK +GE EFWFAIIKVVA++GMI G YLLVSG GGPQAS++NLW Sbjct: 131 AAAFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGTGGPQASVTNLW 190 Query: 190 SHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVIYRILIFYI 249 HGGFFPHG GL +A+IMFSFGGLE++G TAAEAD+P+ IPKA+NQVIYRILIFYI Sbjct: 191 EHGGFFPHGVGGLVMAMAIIMFSFGGLEMLGFTAAEADKPRTVIPKAINQVIYRILIFYI 250 Query: 250 CSLAVLLSLYPWNEVAA---------GGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYN 300 +L VLLSL PW+ + A GSPFV +FS +GS A++LN VVLTAALSVYN Sbjct: 251 GALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSDTAAHILNFVVLTAALSVYN 310 Query: 301 SGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGL 360 SG Y NSRML G+AEQG+AP+AL K+D+RGVP +I SA T V++NYLIP AL L Sbjct: 311 SGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAITLVAVLMNYLIPQHALEL 370 Query: 361 LMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILA 420 LM+LVVA LV+NWA+IS +H K R+ M G+ +FK+ W+P N++CLAF+ ILVI+ Sbjct: 371 LMSLVVATLVINWAMISFSHFKFRQHMNRTGQVPLFKALWYPYGNYVCLAFVVFILVIML 430 Query: 421 MTPGLSVSVLLVPLWLVVMWAGYAFKRRRAAAHVAA 456 M PG+ VSV +P+W++ M Y K +R+A A Sbjct: 431 MIPGIQVSVFAIPVWVMFMAVCYGIKNKRSAQQALA 466 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: 646 Number of extensions: 23 Number of successful extensions: 2 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