Align Proline-specific permease (ProY) (characterized)
to candidate AO353_05965 AO353_05965 aromatic amino acid transporter
Query= TCDB::P37460 (456 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05965 Length = 466 Score = 373 bits (958), Expect = e-108 Identities = 195/459 (42%), Positives = 280/459 (61%), Gaps = 12/459 (2%) Query: 7 LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALGEMS 66 LKRGL RHI+ +ALG AIGTGLF GSA +K AGPS++L Y I G A++IMR LGEM Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMI 70 Query: 67 VHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPHWIW 126 V P A SFS +A G AG+++GW Y ++V +A++TA G Y+ W+P VP W+ Sbjct: 71 VEEPVAGSFSHFAHNYWGSFAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWVS 130 Query: 127 VLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPTGIHN 186 +++ IN M+VKVFGE+EFWF+ KV II MI G ++V G GG + N Sbjct: 131 AAVFFVLVNLINTMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLV--SGTGGPQASVSN 188 Query: 187 LWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILVF 246 LWS+GGFF NG G++M++ +MF++GG+E++GITA EA +P K IP+AIN V R+L+F Sbjct: 189 LWSHGGFFPNGTNGLLMAMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVVYRVLIF 248 Query: 247 YVGTLFVIMSIYPWNQV---------GTNGSPFVLTFQHMGITFAASILNFVVLTASLSA 297 YVG L V++S+YPW+Q+ +GSPFV F +G AA ILNFVVLTA+LS Sbjct: 249 YVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFALIGSNTAAQILNFVVLTAALSV 308 Query: 298 INSDVFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVF 357 NS V+ RML+G+AEQG APK K +++G+P + + + + V +NY+ P Sbjct: 309 YNSGVYCNSRMLYGLAEQGDAPKSLMKLNKQGVPLRALGISALITMLCVVVNYVAPNEAL 368 Query: 358 LVIASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIA 417 ++ +L + + W MI L+ + FR+ + + FK T L F+ II Sbjct: 369 ELLFALVVASLMINWAMISLTHLKFRKAMGQRGI-VPGFKAFWSPYTNYLCLAFMAMIIY 427 Query: 418 LIGYHPDTRISLYVGFAWIVLLLIGWIFKRRRDRQLAQA 456 ++ P R S+Y W+++L + + + R R L+ A Sbjct: 428 VMLLIPGVRASVYAIPVWVLILFVFYRIRVARTRALSVA 466 Lambda K H 0.329 0.143 0.449 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: 582 Number of extensions: 31 Number of successful extensions: 5 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: 456 Length of database: 466 Length adjustment: 33 Effective length of query: 423 Effective length of database: 433 Effective search space: 183159 Effective search space used: 183159 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:
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