Align Proline-specific permease (ProY) (characterized)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter
Query= TCDB::P37460 (456 letters) >FitnessBrowser__WCS417:GFF4632 Length = 467 Score = 368 bits (944), Expect = e-106 Identities = 191/459 (41%), 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 +P W+ Sbjct: 71 VEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWWPDIPTWVS 130 Query: 127 VLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPTGIHN 186 L + + IN ++VK FGE EFWF+ KV I+ MIV G ++ G GG + N Sbjct: 131 ALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLF--SGTGGPQASVSN 188 Query: 187 LWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILVF 246 LWS+GGFF NG +G++MS+ +MF++GG+E++GITA EA +P K IP+AIN V RIL+F Sbjct: 189 LWSHGGFFPNGGMGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVVYRILIF 248 Query: 247 YVGTLFVIMSIYPWNQV---------GTNGSPFVLTFQHMGITFAASILNFVVLTASLSA 297 YVG L V++S+YPW+Q+ +GSPFV F +G AA ILNFVVLTA+LS Sbjct: 249 YVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVVLTAALSV 308 Query: 298 INSDVFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVF 357 NS V+ RML G+AEQG APK K +++G+P + + + + V +NY+ P++ Sbjct: 309 YNSGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVNYVAPQSAL 368 Query: 358 LVIASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIA 417 ++ +L + + W +I ++ I FR+ + + V FK + L F+V II+ Sbjct: 369 ELLFALVVASLMINWALISITHIKFRKAMGEQGVTP-SFKTFWFPFSNYLCLAFMVMIIS 427 Query: 418 LIGYHPDTRISLYVGFAWIVLLLIGWIFKRRRDRQLAQA 456 ++ P S+Y W+ ++ + + + RR + A Sbjct: 428 VMLAIPGISESVYAMPVWVGIIYVAYRLRVRRSHAVVNA 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: 579 Number of extensions: 35 Number of successful extensions: 4 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: 467 Length adjustment: 33 Effective length of query: 423 Effective length of database: 434 Effective search space: 183582 Effective search space used: 183582 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