Align 6-phospho-β-glycosidase (GK3214) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate 16981 b2901 6-phospho-beta-glucosidase A (NCBI)
Query= CAZy::BAD77499.1 (478 letters) >FitnessBrowser__Keio:16981 Length = 479 Score = 363 bits (933), Expect = e-105 Identities = 196/492 (39%), Positives = 284/492 (57%), Gaps = 44/492 (8%) Query: 10 PPGFLWGAASAAYQVEGAWNEDGKGLSVWDVFAKQ-------------PGRTFKGTNGDV 56 P FLWG A AA+QVEG WN+ GKG S+ DV PG+ + Sbjct: 9 PKDFLWGGAVAAHQVEGGWNKGGKGPSICDVLTGGAHGVPREITKEVLPGKYYPNHE--- 65 Query: 57 AVDHYHRYKEDVALMAEMGLKAYRFSVSWSRVFPDGNGAV-NEKGLDFYDRLIEELRTHG 115 AVD Y YKED+ L AEMG K +R S++W+R+FP G+ A NE+GL FYD + +EL + Sbjct: 66 AVDFYGHYKEDIKLFAEMGFKCFRTSIAWTRIFPKGDEAQPNEEGLKFYDDMFDELLKYN 125 Query: 116 IEPIVTLYHWDVPQALMDAYGAWESRRIIDDFDRYAVTLFQRFGDRVKYWVTLNEQNIFI 175 IEP++TL H+++P L+ YG+W +R+++D F R+A +F+R+ +VKYW+T NE N Sbjct: 126 IEPVITLSHFEMPLHLVQQYGSWTNRKVVDFFVRFAEVVFERYKHKVKYWMTFNEINNQR 185 Query: 176 S-----LGYRLG--LHPPGVKDMKRMYEANHIANLANAKVIQSFRHYVPDGKIGPSFAYS 228 + GY ++ + MY+ H +A+A +++ R P+ K+G A Sbjct: 186 NWRAPLFGYCCSGVVYTEHENPEETMYQVLHHQFVASALAVKAARRINPEMKVGCMLAMV 245 Query: 229 PMYPYDSRPENVLAFENAEEFQNHWWMDVYAWGMYPQAAWNYLESQGLEPTVAPGDWELL 288 P+YPY P++V+ F + + + DV G YP N E +G + GD ++L Sbjct: 246 PLYPYSCNPDDVM-FAQESMRERYVFTDVQLRGYYPSYVLNEWERRGFNIKMEDGDLDVL 304 Query: 289 QEAKPDFMGVNYYQTTTVEHNPPDGVSEGVMNTTGKKGTSTSSGIPGLFKTVRNPYVDTT 348 +E D++G +YY T V+ +EG T I G +V NPYV + Sbjct: 305 REGTCDYLGFSYYMTNAVK-------AEG----------GTGDAISGFEGSVPNPYVKAS 347 Query: 349 NWDWAIDPVGLRIGLRRIANRYRLPILITENGLGEFDTLEPDDIVNDDYRIDYLRRHIQE 408 +W W IDPVGLR L + RY+ P+ I ENG G +D +E D +NDDYRIDYLR HI+E Sbjct: 348 DWGWQIDPVGLRYALCELYERYQRPLFIVENGFGAYDKVEEDGSINDDYRIDYLRAHIEE 407 Query: 409 IQRAIT-DGVDVLGYCVWSFTDLLSWLNG-YQKRYGFVYVNRDDESEKDLRRIKKKSFYW 466 +++A+T DGVD++GY W D +S+ G Y KRYGF+YVN+ D+ D+ R +KKSF W Sbjct: 408 MKKAVTYDGVDLMGYTPWGCIDCVSFTTGQYSKRYGFIYVNKHDDGTGDMSRSRKKSFNW 467 Query: 467 YQRVIATNGAEL 478 Y+ VIA+NG +L Sbjct: 468 YKEVIASNGEKL 479 Lambda K H 0.320 0.139 0.448 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: 782 Number of extensions: 42 Number of successful extensions: 8 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: 478 Length of database: 479 Length adjustment: 34 Effective length of query: 444 Effective length of database: 445 Effective search space: 197580 Effective search space used: 197580 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 (21.8 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