Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein
Query= TCDB::G3LHY8 (358 letters) >NCBI__GCF_000009985.1:WP_011382978.1 Length = 553 Score = 125 bits (315), Expect = 2e-33 Identities = 88/242 (36%), Positives = 127/242 (52%), Gaps = 6/242 (2%) Query: 1 MLELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHF 60 +LEL+ AK GA + DL +E G +LG + +GKT+L+ LMAGL +P G + Sbjct: 3 ILELKGVAKSYGASSVLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAGEVLL 62 Query: 61 DGTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVR--KAAEL 118 G V G P R V V+Q + P LTV NIA + DA+ +R+ R K + Sbjct: 63 RGKPVDG-PGADRGV--VFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAKYIGM 119 Query: 119 LKLTPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIF 178 + L+ +R P LSGG +QR A+ARAL + ++L+DEPL+ LD R +L++E+ I+ Sbjct: 120 VGLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEIEAIW 179 Query: 179 AQSGAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLN 238 Q + T + EALLL LN G FGP+ +V P A + +DP Sbjct: 180 EQEKKTVILITNDVDEALLLADRIIPLNPGPGATFGPSFKV-NLPRPRDRAAVNSDPDFK 238 Query: 239 TL 240 L Sbjct: 239 RL 240 Score = 78.2 bits (191), Expect = 5e-19 Identities = 59/216 (27%), Positives = 102/216 (47%), Gaps = 16/216 (7%) Query: 17 IYPT-----------DLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDV 65 IYPT DL + +G L+G + GK++++ + AGL + G + DG +V Sbjct: 301 IYPTPKGPLTVVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGGVILDGREV 360 Query: 66 TGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDRE--VRKAAELLKLTP 123 + + A+V+Q +P LT N+A + A+ +R V E + L Sbjct: 361 SEAGPDR---AVVFQAPSLFPWLTALQNVALGVDRVYPHASPAERLDIVSYYLERVGLGD 417 Query: 124 YLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGA 183 +D+ ++S G +QR +ARA + L+L+DEP LD R EL+E L +++ ++ Sbjct: 418 SMDKKASDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVLMEVWTRTRV 477 Query: 184 IFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEV 219 + T + EA+LL + G + G + V Sbjct: 478 TAICVTHDVDEAILLADKVVMMTNGPNARIGKVLNV 513 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: 467 Number of extensions: 24 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 358 Length of database: 553 Length adjustment: 32 Effective length of query: 326 Effective length of database: 521 Effective search space: 169846 Effective search space used: 169846 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: 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