Align L-alanine and D-alanine permease (characterized)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases
Query= reanno::WCS417:GFF1065 (472 letters) >FitnessBrowser__psRCH2:GFF1660 Length = 464 Score = 400 bits (1027), Expect = e-116 Identities = 204/455 (44%), Positives = 295/455 (64%), Gaps = 16/455 (3%) Query: 11 ETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIM 70 ET G L+R L RHI+L+ALG IG GLFLGSA + AGP+++L Y IGG +IM Sbjct: 4 ETLHTGSLQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPSMILGYAIGGFIAFLIM 63 Query: 71 RALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFP 130 R LGEM V PVAGSFS +A Y G AGFL+GWNYW L+++ +AE+TAV Y+ W+P Sbjct: 64 RQLGEMIVEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWP 123 Query: 131 DTPRWIWALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDG 190 + P W A A + + INL VKAFGE EFWFA++K+ I+ M++ G+ ++ G G G Sbjct: 124 EVPTWATAAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLLVSGKG--G 181 Query: 191 VALGISNLWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSV 250 ISNLW+HGGF PNG G+L++L ++MF++ G+E++G+TA EA P+ IP AI V Sbjct: 182 EQASISNLWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQV 241 Query: 251 FWRILLFYVGALFVILSIYPWNEI---------GTQGSPFVMTFERLGIKTAAGIINFVV 301 +RIL+FY+GAL V+L++YPW+ + GSPFV F +G TAA ++NFVV Sbjct: 242 VYRILIFYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFVV 301 Query: 302 ITAALSSCNGGIFSTGRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNY 361 +TAALS N G++ RMLY LA+ G AP + K +S GVP A+ +S LL V +NY Sbjct: 302 LTAALSVYNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVTLLCVAVNY 361 Query: 362 LVPEKVFVWVTSIATFGAIWTWLMILLAQLKFRKSLSPAEQAGLK--YRMWLYPVSSYLA 419 L P+ + S+A + W MI LA LKFR+++ +Q G++ ++ + +P+S+YL Sbjct: 362 LFPQGALELLMSLAVAALVINWAMISLAHLKFRRAM---QQQGVEPSFKAFWFPLSNYLC 418 Query: 420 LAFLLLVVGLMAYFPDTRIALYVGPVFLVLLTVLF 454 LAF+ ++ +M + P R++++ PV++ L + + Sbjct: 419 LAFVAGILIIMLWLPGIRMSVFAIPVWVGFLWLCY 453 Lambda K H 0.328 0.142 0.447 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: 678 Number of extensions: 42 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 (21.7 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