Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate RR42_RS15935 RR42_RS15935 C4-dicarboxylate ABC transporter
Query= TCDB::P74224 (445 letters) >FitnessBrowser__Cup4G11:RR42_RS15935 Length = 582 Score = 365 bits (937), Expect = e-105 Identities = 202/515 (39%), Positives = 306/515 (59%), Gaps = 80/515 (15%) Query: 1 MVDYDWLGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFG 60 M+ +++ P+MF G +VF+ G+PVAFSL V + F I+ G F FL A+P R+FG Sbjct: 1 MIPLEYMPPLMFGGLVVFMLIGFPVAFSLSAVGLAFGILAIQFGYFPVSFLQAVPSRVFG 60 Query: 61 -IMANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATT 119 ++AN LLAIPFF F+G++LE+ G+AE +L++MG + G +RGGL +VI+VG +L A T Sbjct: 61 SVLANELLLAIPFFTFMGAILEKCGLAEDMLDSMGQLFGPVRGGLGYSVIIVGFILGAIT 120 Query: 120 GVVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQL----- 174 G VAA V+AM +ISLP+M+RY Y+ + A+GV+ ASGT+ Q++PPS+VL+VLADQL Sbjct: 121 GTVAAQVIAMAMISLPVMMRYRYNMKYATGVLAASGTITQLVPPSLVLVVLADQLKTPMG 180 Query: 175 GVSVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVM 234 VG +++G+ P ++ FALY ++ +KPD P +P E R + G L R+ ++ + Sbjct: 181 SADVGSMYLGAWGPSVIQIALFALYTFVLTRIKPDWLPPVPVEERTLRGWPLWRKCLRGI 240 Query: 235 LPPLVLILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQ----RLNWKALWEVCDATLR 290 +P VLI LVLG+I GIA+PTE+GA+G++GA+ LA +L+ + ++ + A Sbjct: 241 IPCAVLIFLVLGTIMLGIATPTESGAMGAVGALVLAVLRDPGFGKLD-RNIYRIGLAATG 299 Query: 291 ITSMVMLILLGSTAFSL--------------------VFRGL------------------ 312 + + + GS AF + RGL Sbjct: 300 VAIIAGTVAFGSHAFRIPLALVYLVITWLLLRAGQLTALRGLIIEAYQSTARITAMVVFI 359 Query: 313 --------------EGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLP 358 +G ++ + +LPGG IGFL + + IF L FF+DFFEIAFIV+P Sbjct: 360 LIGSTCFSVVFQGVDGGAWVEHMFTSLPGGWIGFLLVVNLFIFFLAFFLDFFEIAFIVVP 419 Query: 359 LFKPVA-----------------EALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGV 401 + PVA A L+W+GV++ N+QTSF+ PPFGFALFYLRG+ Sbjct: 420 MLAPVAVKVLAPVVADSMGGNPEAAATAALVWFGVMLCVNMQTSFMHPPFGFALFYLRGI 479 Query: 402 APASLTTGQIYRGAVPFIGLQVLVLLLIIIFPALI 436 AP + + IY GA+P++GLQ+++++L++ +P L+ Sbjct: 480 APKEVKSSDIYWGALPWVGLQMIMVVLVMFWPGLV 514 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: 838 Number of extensions: 53 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 445 Length of database: 582 Length adjustment: 34 Effective length of query: 411 Effective length of database: 548 Effective search space: 225228 Effective search space used: 225228 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