Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate SMc04249 SMc04249 hypothetical protein
Query= TCDB::P74224 (445 letters) >FitnessBrowser__Smeli:SMc04249 Length = 597 Score = 417 bits (1073), Expect = e-121 Identities = 240/507 (47%), Positives = 319/507 (62%), Gaps = 77/507 (15%) Query: 7 LGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSF-DPIFLS-----AMPQRIFG 60 L P+MFV +VFL GYPVAFSL +LF IIG L D I LS A+P+R +G Sbjct: 9 LAPIMFVSLIVFLLLGYPVAFSLAANGLLFFIIGVELAPLSDSINLSWPLLNALPERFWG 68 Query: 61 IMANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTG 120 +M+N TLLAIPFF F+G +LERSG+AE LL+T+G + G +RGGLA AVI VG +LAATTG Sbjct: 69 VMSNDTLLAIPFFTFMGIVLERSGMAEDLLDTIGQLFGPVRGGLAYAVIFVGALLAATTG 128 Query: 121 VVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGD 180 VVAA+V+AMGLISLPIMLRYGY + +ASGVI ASGTL QIIPPS+VLIVLADQLG SVGD Sbjct: 129 VVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVLADQLGRSVGD 188 Query: 181 LFIGSL-----LPGLMMA---------------------------GSFALYVLIIA---- 204 ++ G+L L GL M S A+ +L+ Sbjct: 189 MYAGALIPGLVLTGLYMGYILLMTFVKRHSMPALPLEARTLGSGVASLAIALLVACAIAY 248 Query: 205 ----WLKPD------------------LAPALPAEVRNIGGQELRRRIVQVMLPPLVLIL 242 +L P LA ++ L ++++ V++PPL LI Sbjct: 249 AAHVYLSPTQGENADILGATVGIIFIYLAALADRTLKINALSRLAQQVIIVLIPPLALIF 308 Query: 243 LVLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILLGS 302 LVLG+IF GIA+PTE GA+G++GA+ +A RLN + + +T R+++ V+ IL+G+ Sbjct: 309 LVLGTIFLGIATPTEGGAMGAVGALVMAAGKGRLNMEVVRAALASTTRLSAFVLFILIGA 368 Query: 303 TAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLFKP 362 FSL F G+ G ++ LL LPGG+IGFL + +F L FF+DFFE+AFI++PL P Sbjct: 369 RVFSLTFYGVNGHLWVEHLLTALPGGEIGFLIAVNVLVFFLAFFLDFFELAFIIVPLLAP 428 Query: 363 VAEALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAP-------------ASLTTG 409 A+ L +DLIW+GV++G N+QTSF+ PPFGFALFYLR VA +TTG Sbjct: 429 AADKLGIDLIWFGVLLGINMQTSFMHPPFGFALFYLRSVAARVPYLDRVTGKMMQPVTTG 488 Query: 410 QIYRGAVPFIGLQVLVLLLIIIFPALI 436 QIY GAVPF+ +QV+++ L ++FP ++ Sbjct: 489 QIYWGAVPFVCIQVVMVALTLMFPQMV 515 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: 827 Number of extensions: 50 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 445 Length of database: 597 Length adjustment: 35 Effective length of query: 410 Effective length of database: 562 Effective search space: 230420 Effective search space used: 230420 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