Align 6-P-β-glucosidase (LicH;Gan4C) (EC 3.2.1.86) (characterized)
to candidate SM_b21463 SM_b21463 glycosyl hydrolase, 6-phospho-beta-glucosidase
Query= CAZy::AHL67642.1 (447 letters) >FitnessBrowser__Smeli:SM_b21463 Length = 461 Score = 209 bits (533), Expect = 1e-58 Identities = 145/469 (30%), Positives = 224/469 (47%), Gaps = 55/469 (11%) Query: 5 LKMATIGGGSSYTPELVEGLIKRYHELPVGELWLVDIPEGKEKLEIVGALAKRMVEKAGV 64 +K+ IGGG P V ++R + E+ L DI E KLE+ G +++ + + Sbjct: 1 MKLTLIGGGGVRAPLFVGSALRRAERSGLSEICLQDINE--RKLELFGRISQELARRTQS 58 Query: 65 PIEIHLTLDRRRALEGADFVTTQFRVGGLEARAKDERIPLKYGVIGQETNGPGGLFKGLR 124 P+ I + D RAL+GA +V T R G + R KDERI L +GV+GQET GPGG LR Sbjct: 59 PVRITMAADAERALDGARYVVTTVRPGNEDGRIKDERIALAHGVLGQETTGPGGFAMALR 118 Query: 125 TIPVILDIIRDMEELCPDAWLINFTNPAGMVTEAVLRYTKQEKVVGLCNVPIGMRMGVAK 184 +IPVIL ++++ PDAWL NFTNPAG+VT+A L+ + VG+C+ G + +A Sbjct: 119 SIPVILKYAEILKKVSPDAWLFNFTNPAGLVTQA-LQNEGYHRTVGICDGANGAQEALAH 177 Query: 185 LLGVDADRVHIDFAGLNHMVFGLHVYLDGVEVTEKVIDLVAHPDRSGVTMKNIVDLGWEP 244 V + V + GLNH+ F +DG EV + ++D +++ ++ Sbjct: 178 WHKVQQNDVRCEVYGLNHLSFTRRATIDGKEVLQPLLD-------DDGFLRSTSQRMFDA 230 Query: 245 DFLKGLKVLPCPYHRYYYQTDKMLAEELEAAKTKG-TRAEVVQQLEKELF---------- 293 ++ + Y YYY +K +EA K TR E V+ L L Sbjct: 231 SLIRSQRNWINEYLYYYYYAEK----AVEALKADARTRGEEVKDLNAALITRLSAMDLNA 286 Query: 294 --ELYKDPNLAIK--------------PPQLEQ--------------RGGAYYSDAACSL 323 E PN A + P +E+ G Y+ A +L Sbjct: 287 DAERRSPPNYAYERRRNATYMHYALTDAPSMEEADRLVEGLAAAQTGEEGEGYAGVALNL 346 Query: 324 ISSIYNDKRDIQPVNTRNNGAIASIPPESAVEVNCVITKDGPKPIAVGDLPVAVRGLVQQ 383 + ++ K +N RN GAI + + VEV+C++ +G +P+ +G +P A +V Sbjct: 347 VDALETGKPCYTGLNVRNEGAIEGLRNDDVVEVSCLVDGEGIRPLKIGAMPEAQSQIVHN 406 Query: 384 IKSFERVAAEAAVTGDYQTALVAMTINPLVPSDTIAKQMLDEMLEAHKE 432 +K +ER+A A A+ A+ +PLV S + A ++DE L AH E Sbjct: 407 VKRYERLAVRAIRERSRDLAVQALMAHPLVLSYSRAVPLVDEYLAAHAE 455 Lambda K H 0.319 0.138 0.402 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: 462 Number of extensions: 13 Number of successful extensions: 3 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: 447 Length of database: 461 Length adjustment: 33 Effective length of query: 414 Effective length of database: 428 Effective search space: 177192 Effective search space used: 177192 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