Align Proline-specific permease (ProY) (characterized)
to candidate RR42_RS33495 RR42_RS33495 aromatic amino acid transporter
Query= TCDB::P37460 (456 letters) >FitnessBrowser__Cup4G11:RR42_RS33495 Length = 465 Score = 393 bits (1009), Expect = e-114 Identities = 206/447 (46%), Positives = 285/447 (63%), Gaps = 7/447 (1%) Query: 7 LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALGEMS 66 LKRGL RHI+ +ALG AIGTGLF G A IKMAGPSVLL Y + G+ A+ IMR LGEM Sbjct: 13 LKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLGEMV 72 Query: 67 VHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPHWIW 126 V P A SFS +A + G AG+++GW Y ++V++A+++A GIY+ W+P +P W Sbjct: 73 VDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPTWAS 132 Query: 127 VLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPTGIHN 186 L L+I AINL SVK FGE+EFWFS KV I+ MIV G ++ G G + N Sbjct: 133 ALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLA--SGTAGPQASVSN 190 Query: 187 LWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILVF 246 LW +GGFF NG G++M++ ++MF++GG+E++GITA EA +PEK+IP+A N V RIL+F Sbjct: 191 LWQHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQVIYRILIF 250 Query: 247 YVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVFGVG 306 YVG L V++S+YPW +V T GSPFVL F M A++LN VVLTA+LS NS V+ Sbjct: 251 YVGALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYNSGVYCNS 310 Query: 307 RMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVIASLATF 366 RML G+A+QG+APK K ++RGIP + V +A V +NY MP F ++ L Sbjct: 311 RMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEAFELLMGLVVS 370 Query: 367 ATVWVWIMILLSQIAFRR--RLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIGYHPD 424 A + W MI + + FRR R +E +FK G +T L FL I+ ++ P Sbjct: 371 ALIINWAMISIIHLKFRRDKRAAGQET---RFKSLGYPLTNYVCLAFLAGILYVMYLTPG 427 Query: 425 TRISLYVGFAWIVLLLIGWIFKRRRDR 451 RIS+Y+ AW+ +L + + ++++ R Sbjct: 428 LRISVYLIPAWLAVLGLSYRLRQKQKR 454 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: 584 Number of extensions: 30 Number of successful extensions: 3 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: 465 Length adjustment: 33 Effective length of query: 423 Effective length of database: 432 Effective search space: 182736 Effective search space used: 182736 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