Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate 202250 SO3136 C4-dicarboxylate transport protein (NCBI ptt file)
Query= TCDB::P74224 (445 letters) >FitnessBrowser__MR1:202250 Length = 465 Score = 187 bits (474), Expect = 8e-52 Identities = 134/469 (28%), Positives = 230/469 (49%), Gaps = 53/469 (11%) Query: 11 MFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMANG-TLLA 69 +F + + G P+A +LG ++L + F L+++ +++ + TLLA Sbjct: 6 LFCVLFICMFLGMPIAIALGFSSMLTILF------FSNDSLASVALKLYESSSEHYTLLA 59 Query: 70 IPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATVVAM 129 IPFFI + L G+A ++++ +GH+RGGLA+A ++ + AA +G ATV A+ Sbjct: 60 IPFFILSSAFLSTGGVARRIIDFAMDCVGHIRGGLAMASVMACMLFAAVSGSSPATVAAI 119 Query: 130 GLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGDLFIGSLLPG 189 G I + M++ GY ++ ASGVI SGTLG +IPPS+V++V A VSV +F+ L+PG Sbjct: 120 GSIVIVGMVKAGYPEKFASGVITTSGTLGILIPPSIVMLVYAAATEVSVAKIFMAGLVPG 179 Query: 190 LMMAGSFALYVLIIAWLKPDLAPALP-AEVRNIGGQELRRRIVQVMLPPLVLILLVLGSI 248 L++ + + I+A +K P++P + +G + + L LI +VLGSI Sbjct: 180 LLLGFLIMVVIYIVARIKN--LPSIPFPGFKKLGVSSAK------AIGGLALIFIVLGSI 231 Query: 249 FFGIASPTEAGAVGSIGAIALAHFNQR-------LNW----------------------- 278 + G+ASPTEA AV + A +A F R + W Sbjct: 232 YGGVASPTEASAVACVYAYFIAVFGYRDIGPLKNVAWRNPNEAIPSAIARNLGHMVLGLI 291 Query: 279 -----KALWEVCDATLRITSMVMLILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFL 333 K + V +++ M++ I+ + F+ V + + + + GFL Sbjct: 292 KTPIDKEIRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAEYIVGMGLPAWGFL 351 Query: 334 AISMITIFILGFFIDFFEIAFIVLPLFKPVAEALNLDLIWYGVIVGANLQTSFLTPPFGF 393 I + + G F++ I I+ P+ P+A L +D I G+I+ N++ LTPP G Sbjct: 352 IIVNLLLLAAGNFMEPSAIVLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGL 411 Query: 394 ALFYLRGVAPASLTTGQIYRGAVPFIGLQVLVLLLIIIFPALINWLPSL 442 LF G+ ++ G + + +P++ + L+LI P + +LP L Sbjct: 412 NLFVTSGITGRNI--GWVIQSVLPWLVFMLAFLMLITYVPQISLFLPEL 458 Score = 29.6 bits (65), Expect = 2e-04 Identities = 31/119 (26%), Positives = 55/119 (46%), Gaps = 8/119 (6%) Query: 108 VILVGTMLAATTGVV--AATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPP-S 164 +I+V +L A + +A V+ M I PI + G ++V + +G + PP Sbjct: 351 LIIVNLLLLAAGNFMEPSAIVLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVG 410 Query: 165 VVLIVLADQLGVSVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGG 223 + L V + G ++G I S+LP L+ F L L++ P ++ LP + + G Sbjct: 411 LNLFVTSGITGRNIG-WVIQSVLPWLV----FMLAFLMLITYVPQISLFLPELLDKLNG 464 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: 514 Number of extensions: 23 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 445 Length of database: 465 Length adjustment: 33 Effective length of query: 412 Effective length of database: 432 Effective search space: 177984 Effective search space used: 177984 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: 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