Align The amino acid (leucine):2 Na+ symporter, LeuTAa (Yamashita et al., 2005). LeuT possesses two ion binding sites, NA1 and NA2, both highly specific for Na+ but with differing mechanisms of binding (Noskov and Roux, 2008). X-ray structures have been determined for LeuT in substrate-free outward-open and apo inward-open states (characterized)
to candidate 8500111 DvMF_0874 sodium:neurotransmitter symporter (RefSeq)
Query= TCDB::O67854 (513 letters) >FitnessBrowser__Miya:8500111 Length = 454 Score = 193 bits (491), Expect = 1e-53 Identities = 147/475 (30%), Positives = 240/475 (50%), Gaps = 49/475 (10%) Query: 5 REHWATRLGLILAMAGNAVGLGNFLRFPVQAAENGGGAFMIPYIIAFLLVGIPLMWIEWA 64 R+ +ATRLG++ A G+AVGLGN +FP +NGG +F++ Y++A LLVG+P+M E Sbjct: 9 RDGFATRLGVLAATLGSAVGLGNIWKFPALTGQNGGASFLLVYVLATLLVGLPVMISEIM 68 Query: 65 MGRYGGAQGHGTTPAIFYLLWRNRFAKILGVFGLWIPLVVAIYYVYIESWTLGFAIKFLV 124 +GR A GT L + + ++G G+ ++ +Y + W + K L Sbjct: 69 LGRRARANAVGT---FRQLAPKGQPWHLVGFSGVVAAFLIMGFYTDVAGWVFAYIFKSLS 125 Query: 125 GLVPEPPPNATDPDSILRPFKEFLYSYIGVPKGDEPILKPSLFAYIVFLITMFINVSILI 184 G + TDP + F+ + +G P ++ L+ + V ++ I+V I+I Sbjct: 126 GEIA-----TTDPAVAAKAFE----ALVGDP------VQSLLWQWGVLVL---ISV-III 166 Query: 185 RGISKGIERFAKIAMPTLFILAVFLVIRVFLLETPNGTAADGLNFLWTPDFEKLKDPGVW 244 G+++GIER K+ MP L +L V + R L AA+GL FL+TPDF K+ PGV Sbjct: 167 AGVAQGIERTTKVLMPVLLLLLVAVCARSLTLP----KAAEGLAFLFTPDFSKI-TPGVI 221 Query: 245 IAAVGQIFFTLSLGFGAIITYASYVRKDQDIVLSGLTAATLNEKAEVILGGSISIPAAVA 304 + A+G FF LS+G G + TY SY R DQDI L+ T L + IL G PA Sbjct: 222 LMALGLAFFKLSIGMGTMTTYGSYFRNDQDIPLTA-TRVMLCDLTISILAGMAVFPAVFN 280 Query: 305 FFGVANAVAIAKAGAFNLGFITLPAIFSQTAGGTFLGFLWFFLLFFAGLTSSIAIMQPMI 364 F + +L F+T+PA+F+ GG ++F L A + +++++ + Sbjct: 281 F-------GFEPSAGPSLLFMTIPAVFTSLPGGQVFMVIFFCLTAIAATGAMLSLLEVPV 333 Query: 365 AFLEDELKLSRKHAVLWTA---AIVFFSAHLVM--------FLNKSLDEMDFWAGTIGVV 413 A+L + + RK A + T+ AI+ A L M F D DF + + + Sbjct: 334 AWLAESFGMPRKRATILTSVTLAIIGLPATLSMSTMANVKIFGMTVFDLYDFLSSNVLLP 393 Query: 414 FFGLTELIIFFWIFGADKAWEEI-NRGGIIKVPRI--YYYVMRYITPAFLAVLLV 465 G+ + W++GA E+ NRG ++ P I + V+R+++P + ++L+ Sbjct: 394 VGGIFICLFAGWVWGAANVKTELSNRGQLLNGPIIAAFLTVVRWVSPVLVLLVLL 448 Lambda K H 0.330 0.146 0.463 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: 619 Number of extensions: 34 Number of successful extensions: 5 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: 513 Length of database: 454 Length adjustment: 34 Effective length of query: 479 Effective length of database: 420 Effective search space: 201180 Effective search space used: 201180 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 52 (24.6 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