Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate 3610014 Dshi_3395 TRAP C4-dicarboxylate transport system permease DctM subunit (RefSeq)
Query= TCDB::P74224 (445 letters) >FitnessBrowser__Dino:3610014 Length = 482 Score = 347 bits (889), Expect = e-100 Identities = 181/461 (39%), Positives = 292/461 (63%), Gaps = 30/461 (6%) Query: 11 MFVGALVFLGCGYPVAFSLGGVAILFAIIGAAL-----GSFDPIF-----------LSAM 54 MF+ + L G PVA++L GV+++FA++ +F I L + Sbjct: 21 MFLVFIYLLFRGIPVAYALVGVSLIFALVAEIFLDPNRAAFRDIIEFDRTGIDYQRLQVL 80 Query: 55 PQRIFG-IMANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGT 113 R+FG I+ N L+A+P FIF+G ML++SG+A++++ +M + G LRGGL+L V+L+G Sbjct: 81 SGRLFGNIVKNPVLVALPMFIFMGLMLDQSGVAQRMMHSMQKLFGGLRGGLSLTVMLIGI 140 Query: 114 MLAATTGVVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQ 173 +LAA+TGV+ A+V +G+++LP M++ YSK +A+G I ++GTLG +IPPS++L++++DQ Sbjct: 141 ILAASTGVIGASVTLLGVMALPAMMQQNYSKPIATGTIASAGTLGILIPPSIMLVIMSDQ 200 Query: 174 LGVSVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQV 233 L +S+GDLF+G+L PGL++ + ++++ + P PA P + + G ++ + ++ Sbjct: 201 LAISLGDLFMGALFPGLILGALYIIFIIAYGLINPKAMPA-PPQTDEV-GWDVVKDVLLA 258 Query: 234 MLPPLVLILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITS 293 ++PP+ LILLVLGSIF G A+PTEA +G++GA LA N RLN+K L EV +TL + Sbjct: 259 VVPPMFLILLVLGSIFAGFATPTEASGLGALGATLLALANGRLNFKVLKEVSRSTLNTSG 318 Query: 294 MVMLILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIA 353 ++ I L + F+LV R GD + + + + + IF+LGF +D+ EI Sbjct: 319 YIVGIFLAANFFALVLRRYGGDEIIQGYVLSTFSDPYMIVLFILFIIFLLGFLLDWIEIT 378 Query: 354 FIVLPLFKPVAEALNL-----------DLIWYGVIVGANLQTSFLTPPFGFALFYLRGVA 402 I++PL P+ L+L ++W+ ++V LQTSFLTPP GFALFYL+GV Sbjct: 379 IIIMPLMLPIIVGLDLAVPGFDQVRDPAVVWFAILVAVTLQTSFLTPPVGFALFYLKGVC 438 Query: 403 PASLTTGQIYRGAVPFIGLQVLVLLLIIIFPALINWLPSLS 443 P ++ G IY+G +PF+ LQ+L L ++ FPAL WLP+++ Sbjct: 439 PPGVSLGHIYKGIIPFVMLQLLGLFIVFQFPALTTWLPAIA 479 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: 708 Number of extensions: 41 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: 445 Length of database: 482 Length adjustment: 33 Effective length of query: 412 Effective length of database: 449 Effective search space: 184988 Effective search space used: 184988 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