Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate BPHYT_RS27955 BPHYT_RS27955 ABC transporter ATP-binding protein
Query= TCDB::G3LHY8 (358 letters) >FitnessBrowser__BFirm:BPHYT_RS27955 Length = 345 Score = 200 bits (508), Expect = 5e-56 Identities = 129/356 (36%), Positives = 182/356 (51%), Gaps = 21/356 (5%) Query: 2 LELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFD 61 ++LRN +K G + + + G VLLGP+ AGKT+ +RL+AGL+RP G + D Sbjct: 4 IQLRNVSKRFGDIVAVDDLSIDVMDGEFVVLLGPSGAGKTTTLRLIAGLERPDAGDVLID 63 Query: 62 GTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDA--ATIDREVRKAAELL 119 G TG+ R+VA ++QQ+ YP LTV+ N+A P+R + + A + V AE+L Sbjct: 64 GGIATGVHPSDRDVAFIFQQYSLYPHLTVFGNLAFPLRSPRRRSSEAEVRARVHAVAEML 123 Query: 120 KLTPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFA 179 + LD +LSGG+ QR A+ RALV+ + LMDEPL++LD KLREELR EL ++ Sbjct: 124 HMESKLDNMATHLSGGEMQRVAIGRALVRQPKVFLMDEPLSSLDAKLREELRIELKRLHR 183 Query: 180 QSGAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNT 239 GA +Y T + EA L L+QGR+ Q G EVY PV+L+ A PP+N Sbjct: 184 AIGATIIYVTHDQVEATTLADRIGILDQGRLVQLGTPREVYGNPVSLSAAQRLGSPPINL 243 Query: 240 LDVTKSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGL-APQTGDAARLQ--ART 296 L P +LA +P G T+A P + L P GDA +Q Sbjct: 244 LP----------------PTLLNLAHIPAGTTTVAIRPEDIVLHDPDVGDARGVQDALNL 287 Query: 297 LVSEITGSESFVHLEYDGVRWVMLAHGIHDIDPDMEVEAFLDTRHLMAFGSDGRAI 352 V E + + L+ G V+ + P V L R L+ F +DGR I Sbjct: 288 TVLEYSPLRHLLILDRAGTAVVVTTVAERNFSPGQSVGVSLPARSLLYFRADGRRI 343 Lambda K H 0.319 0.136 0.392 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: 313 Number of extensions: 17 Number of successful extensions: 3 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: 358 Length of database: 345 Length adjustment: 29 Effective length of query: 329 Effective length of database: 316 Effective search space: 103964 Effective search space used: 103964 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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