Align Proline-specific permease (ProY) (characterized)
to candidate N515DRAFT_3653 N515DRAFT_3653 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= TCDB::P37460 (456 letters) >FitnessBrowser__Dyella79:N515DRAFT_3653 Length = 453 Score = 487 bits (1254), Expect = e-142 Identities = 232/437 (53%), Positives = 313/437 (71%), Gaps = 5/437 (1%) Query: 7 LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALGEMS 66 L+R L+ RHI FMALG AIG GLF GSA+AI +AGPSVL AY+ GG +IIMRALGEM+ Sbjct: 5 LQRRLTPRHITFMALGMAIGAGLFLGSANAINLAGPSVLFAYLFGGAMIFIIMRALGEMA 64 Query: 67 VHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPHWIW 126 VH+P A SFS YA LGP AGY+TGW Y ++ V +A+ TA GIYM WFP +P WIW Sbjct: 65 VHDPVAGSFSTYAHRYLGPFAGYLTGWNYWILMVGVGMAESTAVGIYMRQWFPELPQWIW 124 Query: 127 VLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPTGIHN 186 V V +I +NLM+VKV+GE+EFWF+ KV T+++MI+ G G+I G GNGGQP G+ N Sbjct: 125 VFGSVAMIGGLNLMAVKVYGEMEFWFTLIKVVTVVLMILGGAGMIWLGWGNGGQPVGLAN 184 Query: 187 LWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILVF 246 LWS+GG+F +G+ GM+++L +V+FA+GGIE IG+ AGEA PE++IPRA+NSV RIL+F Sbjct: 185 LWSHGGWFPHGFTGMVLALPVVVFAFGGIETIGMAAGEAAQPERTIPRAVNSVLWRILIF 244 Query: 247 YVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFGVG 306 YVG LFVIM+IYPW+Q+GT GSPFV TF +GI AA ++NFVV+TA+LS NS F Sbjct: 245 YVGALFVIMAIYPWDQLGTQGSPFVTTFGKLGIPQAAGLINFVVITAALSGFNSTTFSGS 304 Query: 307 RMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVIASLATF 366 RML+ ++ + AP + S G+P VLV L+F V LNY++PE +F ++ S+ F Sbjct: 305 RMLYSLSTKAQAPAFLGQVSEHGVPVRAVLVTLACLVFGVVLNYLLPERIFAMMMSILAF 364 Query: 367 ATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIGYHPDTR 426 TVW W+M+L++ +FRRR A F + +T++ L+FL F++ ++GY DTR Sbjct: 365 NTVWTWMMVLIAHYSFRRR-----HGATAFPLRAWPLTSVVCLLFLAFVLFMLGYSADTR 419 Query: 427 ISLYVGFAWIVLLLIGW 443 ++LYVG W+VLL + + Sbjct: 420 VALYVGAGWVVLLSLAY 436 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: 723 Number of extensions: 37 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: 456 Length of database: 453 Length adjustment: 33 Effective length of query: 423 Effective length of database: 420 Effective search space: 177660 Effective search space used: 177660 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