Align Proline-specific permease (ProY) (characterized)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases
Query= TCDB::P37460 (456 letters) >FitnessBrowser__psRCH2:GFF1660 Length = 464 Score = 378 bits (970), Expect = e-109 Identities = 201/459 (43%), Positives = 291/459 (63%), Gaps = 15/459 (3%) Query: 7 LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALGEMS 66 L+RGL RHI+ +ALG AIGTGLF GSA ++ AGPS++L Y IGG A++IMR LGEM Sbjct: 11 LQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPSMILGYAIGGFIAFLIMRQLGEMI 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 VEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWAT 130 Query: 127 VLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQPTGIHN 186 + ++I INL +VK FGE EFWF+ KVA I+ MI+ G+ ++V G GG+ I N Sbjct: 131 AAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLLV--SGKGGEQASISN 188 Query: 187 LWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRILVF 246 LWS+GGFF NG+ GM+++L ++MF++GG+E++GITA EA +P+ IP+AIN V RIL+F Sbjct: 189 LWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQVVYRILIF 248 Query: 247 YVGTLFVIMSIYPWNQV---------GTNGSPFVLTFQHMGITFAASILNFVVLTASLSA 297 Y+G L V++++YPW+ + +GSPFV F +G AA +LNFVVLTA+LS Sbjct: 249 YIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFVVLTAALSV 308 Query: 298 INSDVFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVF 357 NS V+ RML+G+AEQG AP+ K + RG+P + V V + L V +NY+ P+ Sbjct: 309 YNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVTLLCVAVNYLFPQGAL 368 Query: 358 LVIASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIA 417 ++ SLA A V W MI L+ + FRR + + V+ FK ++ L F+ I+ Sbjct: 369 ELLMSLAVAALVINWAMISLAHLKFRRAMQQQGVEP-SFKAFWFPLSNYLCLAFVAGILI 427 Query: 418 LIGYHPDTRISLYVGFAWIVLLLIGWIFKRRRDRQLAQA 456 ++ + P R+S++ W+ L W+ R R R LA+A Sbjct: 428 IMLWLPGIRMSVFAIPVWVGFL---WLCYRLRARLLARA 463 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: 581 Number of extensions: 29 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: 464 Length adjustment: 33 Effective length of query: 423 Effective length of database: 431 Effective search space: 182313 Effective search space used: 182313 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