Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate GFF1982 PGA1_c20160 TRAP transporter, subunit DctM
Query= TCDB::P74224 (445 letters) >FitnessBrowser__Phaeo:GFF1982 Length = 785 Score = 154 bits (390), Expect = 7e-42 Identities = 130/412 (31%), Positives = 192/412 (46%), Gaps = 94/412 (22%) Query: 102 GGLALAVILVGTMLAAT--TGVVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQ 159 GG+ A L L A + AA + GL L +++ G + GV +S Sbjct: 394 GGVTQATKLTEEELEAAKIAKIDAAAPIGTGLTVLMVLM--GLVLAVGRGVSPSSDPKPL 451 Query: 160 IIPP-SVVLIVLADQLGVSVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPA-- 216 I+ V+LI L D + ++ + PG+ VL+IA P L A Sbjct: 452 ILGAIGVLLIALVDVVAIAP------TTSPGIT--------VLLIA------LPTLLALY 491 Query: 217 EVRNIGGQELRRRIVQVMLPPLVLILLVLGSIFFGIASPTEA------GAV--------- 261 R G+ R +++V+ PPL+LI+ VLGSI GI +PT A GA+ Sbjct: 492 GCRIAAGRSARNDLIRVVFPPLILIVAVLGSILGGITNPTPAAALGAGGAIMLAAYRKLQ 551 Query: 262 --GSIGAIAL-------------AHFNQRLNWKA-------------------------- 280 G G I + +F+ R+N ++ Sbjct: 552 DQGKSGKIIIWATFAVAICILVGVNFDLRINGRSGVSAETVIAFGVAYGAYLFALFGLLY 611 Query: 281 ----------LWEVCDATLRITSMVMLILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQI 330 L V T ++TSMV IL+GS +LV G+ ++ L + Sbjct: 612 GCWVLFKGGVLTPVVRETAKVTSMVFTILIGSQLLNLVVISFGGEHYIQQFLKSFDSELK 671 Query: 331 GFLAISMITIFILGFFIDFFEIAFIVLPLFKPVAEALNLDLIWYGVIVGANLQTSFLTPP 390 FL + M+ +FILGF +DF EI +IV+P+ PV + D W ++V NLQTSFLTPP Sbjct: 672 VFLIV-MVVLFILGFVLDFLEIIYIVIPIVGPVIYGGSFDPKWVTIMVAVNLQTSFLTPP 730 Query: 391 FGFALFYLRGVAPASLTTGQIYRGAVPFIGLQVLVLLLIIIFPALINWLPSL 442 FGFALFYLRGVAP +TT IYRG +PF+ +QV+ L ++ +FP+++ +P+L Sbjct: 731 FGFALFYLRGVAPKEVTTAHIYRGVLPFVLIQVVGLGILWMFPSIVTIVPAL 782 Score = 152 bits (385), Expect = 3e-41 Identities = 89/195 (45%), Positives = 118/195 (60%), Gaps = 28/195 (14%) Query: 51 LSAMPQRIFGIMANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVIL 110 ++ M +R+ + TLLA+ F+ +G LERS IA LL TM + G L GGLA+++++ Sbjct: 110 VNRMNERVLAGASIETLLAVLMFVLMGITLERSKIANDLLTTMARVFGPLPGGLAVSIVV 169 Query: 111 VGTMLAATTGVVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVL 170 VG LAA+TG+V ATVV MGL++LP MLR YS ELA+GVI ASGTLGQIIPPS+V+++L Sbjct: 170 VGAFLAASTGIVGATVVTMGLLALPTMLRNNYSPELATGVIAASGTLGQIIPPSIVIVLL 229 Query: 171 ADQLG----------------------------VSVGDLFIGSLLPGLMMAGSFALYVLI 202 G VSVG LF +LLPG+M+A +ALY Sbjct: 230 GTLAGDLYSTAQEARAQEFGCSDALTYLGEPAVVSVGTLFQAALLPGIMLALLYALYAFG 289 Query: 203 IAWLKPDLAPALPAE 217 A L P+ APA+ E Sbjct: 290 YALLNPEKAPAVVLE 304 Lambda K H 0.331 0.148 0.443 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: 911 Number of extensions: 42 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 4 Length of query: 445 Length of database: 785 Length adjustment: 37 Effective length of query: 408 Effective length of database: 748 Effective search space: 305184 Effective search space used: 305184 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: 53 (25.0 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