Align Proline-specific permease (ProY) (characterized)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily
Query= TCDB::P37460 (456 letters) >FitnessBrowser__Dyella79:N515DRAFT_2630 Length = 454 Score = 540 bits (1391), Expect = e-158 Identities = 257/441 (58%), Positives = 337/441 (76%) Query: 1 MESNNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMR 60 M++N+ L+RGL RHIR MALGSAIG GLF GSA+AI++AGP++LL+Y++GGVA +IIMR Sbjct: 1 MQTNDSLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMR 60 Query: 61 ALGEMSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPA 120 ALGEM+V NP A SFSRYAQ+ LGPL GY+TGW Y F L+ IA++TA G+YMGVWFP Sbjct: 61 ALGEMAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPD 120 Query: 121 VPHWIWVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQ 180 VP WIW L+ ++ + A+NL +VK +GE EFWF+ KV TI++MIV G +IV+G+GN G Sbjct: 121 VPQWIWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGV 180 Query: 181 PTGIHNLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVP 240 PTGI NLW++GGF NG GM+M+LQMVMFAY G+E+IG+TAGEA +P+KSIP AINSV Sbjct: 181 PTGISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVF 240 Query: 241 MRILVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINS 300 RIL+FYVG LFVIMSIYPWN++GT+GSPFV+TF+ +GI AA I+NFVVLTA+LS+ N Sbjct: 241 WRILIFYVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVLTAALSSCNG 300 Query: 301 DVFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVI 360 ++ GRML +A+QG AP+ FA TS GIP VLV +ALLF V LNY++P VF+ + Sbjct: 301 GIYSTGRMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPAKVFVWV 360 Query: 361 ASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIG 420 S ATF +W W ++L++Q+ +RR L + L F++P + L FLV ++ L+G Sbjct: 361 TSAATFGAIWTWGIVLITQMKYRRGLSEAQRSQLVFRMPFFPYASYLALAFLVLVVGLMG 420 Query: 421 YHPDTRISLYVGFAWIVLLLI 441 Y PDTR++L VG W+VLL + Sbjct: 421 YFPDTRVALIVGPLWLVLLTV 441 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: 699 Number of extensions: 32 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: 456 Length of database: 454 Length adjustment: 33 Effective length of query: 423 Effective length of database: 421 Effective search space: 178083 Effective search space used: 178083 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