Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate BWI76_RS04870 BWI76_RS04870 aromatic amino acid transporter AroP
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__Koxy:BWI76_RS04870 Length = 455 Score = 653 bits (1684), Expect = 0.0 Identities = 316/451 (70%), Positives = 368/451 (81%) Query: 1 MDNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFM 60 M+ D LKRGLKNRHIQLIALGGAIGTGLFLGSASV+Q AGP +ILGYAI G IAF+ Sbjct: 1 MEGQQHGDRLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQNAGPGIILGYAIAGFIAFL 60 Query: 61 IMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYW 120 IMRQLGEMV +EPVAGSFSHFAYKYWG F GF SGWNYWVLYVLV+MAELTAVG YV +W Sbjct: 61 IMRQLGEMVVEEPVAGSFSHFAYKYWGGFAGFASGWNYWVLYVLVAMAELTAVGKYVQFW 120 Query: 121 WPGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGG 180 WP +PTWVSA + F INAINL NVK +GE EFWFAIIKVVAV+ MILFGG+LL SG+GG Sbjct: 121 WPEIPTWVSAAIFFIAINAINLTNVKVFGEMEFWFAIIKVVAVVAMILFGGWLLFSGNGG 180 Query: 181 PQASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQV 240 PQA++ NLW GGF PHGF GL M+A+IMFSFGGLEL+GITAAEAD P++SIPKA NQV Sbjct: 181 PQATVRNLWEQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQV 240 Query: 241 IYRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYN 300 IYRILIFY+ SLAVLLSL PW+ V A SPFV+IF ++G T AN LN+VVLTAALSVYN Sbjct: 241 IYRILIFYVGSLAVLLSLLPWSRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYN 300 Query: 301 SGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGL 360 S VY NSRML+GLA+QGNAP+ALM VD+RGVP I +SAL T CV++NY P A GL Sbjct: 301 SCVYCNSRMLFGLAQQGNAPKALMSVDKRGVPVNTILVSALVTALCVLINYFAPESAFGL 360 Query: 361 LMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILA 420 LMALVV+ALV+NWA+ISL H+K RRA G F + +P+SNWICL FMA +LVI+ Sbjct: 361 LMALVVSALVINWAMISLAHIKFRRAKQQQGVVTRFPALLYPLSNWICLLFMAGVLVIML 420 Query: 421 MTPGLSVSVLLVPLWLVVMWAGYAFKRRRAA 451 MTPG+++SV L+P+W+ V+ GY FK++ A+ Sbjct: 421 MTPGMAISVYLIPVWIAVLGVGYLFKQKTAS 451 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: 25 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: 455 Length adjustment: 33 Effective length of query: 428 Effective length of database: 422 Effective search space: 180616 Effective search space used: 180616 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