Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__psRCH2:GFF1660 Length = 464 Score = 400 bits (1029), Expect = e-116 Identities = 199/447 (44%), Positives = 297/447 (66%), Gaps = 12/447 (2%) Query: 19 LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78 L RGLK+RHIQ+IA+GGAIG GLFLG+ + AGP ++L YAIGG F IMR LGE++ Sbjct: 11 LQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPSMILGYAIGGFIAFLIMRQLGEMI 70 Query: 79 LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138 + PV+GSF+ +A ++ G +AGF +GW+YW ++V+ GMAE+TAV YV +W+P+VP W Sbjct: 71 VEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWAT 130 Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFSN 198 A A ++ L+N V FGE EFWFA++KV IV MI++GL ++ G G AS SN Sbjct: 131 AAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLLVSGKG--GEQASISN 188 Query: 199 LWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILIF 258 LW+HGGF P G G++L L I+MF++ G+EL+G+TA EA P+ V+P A N VV+RILIF Sbjct: 189 LWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQVVYRILIF 248 Query: 259 YVGALIIMMALVPWNELKPGV---------SPFVYVFERIGVPGAAAIVNLVVITAAASS 309 Y+GAL +++AL PW+ L + SPFV +F IG AA ++N VV+TAA S Sbjct: 249 YIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFVVLTAALSV 308 Query: 310 CNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVF 369 NSG++ RMLY LA+ G APR+ +++S+ VP +A+ SA + + V +NY+ P+ Sbjct: 309 YNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVTLLCVAVNYLFPQGAL 368 Query: 370 VWVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAV 429 + S+++ + W++I +AHL +R+A+ V+ +F+ P +N+L +AF+ + + Sbjct: 369 ELLMSLAVAALVINWAMISLAHLKFRRAMQQQGVEP-SFKAFWFPLSNYLCLAFVAGILI 427 Query: 430 LLSLDPGTRVALYVAPVWFALLGIGYR 456 ++ PG R++++ PVW L + YR Sbjct: 428 IMLWLPGIRMSVFAIPVWVGFLWLCYR 454 Lambda K H 0.328 0.142 0.445 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: 731 Number of extensions: 32 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: 472 Length of database: 464 Length adjustment: 33 Effective length of query: 439 Effective length of database: 431 Effective search space: 189209 Effective search space used: 189209 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