Align 6-phospho-β-glycosidase (GK3214) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate BWI76_RS19550 BWI76_RS19550 phospho-cellobiase
Query= CAZy::BAD77499.1 (478 letters) >FitnessBrowser__Koxy:BWI76_RS19550 Length = 464 Score = 348 bits (893), Expect = e-100 Identities = 197/487 (40%), Positives = 277/487 (56%), Gaps = 39/487 (8%) Query: 6 LKPFPPGFLWGAASAAYQVEGAWNEDGKGLSVWDVFAKQPGRTF-------KGTNG--DV 56 +K FP FLWG A+AA QVEGA+ EDGKGL+ DV QP F G +G D+ Sbjct: 1 MKTFPQAFLWGGATAANQVEGAYLEDGKGLTTSDV---QPRGVFGDVVERVPGDSGIKDI 57 Query: 57 AVDHYHRYKEDVALMAEMGLKAYRFSVSWSRVFPDGNGAV-NEKGLDFYDRLIEELRTHG 115 A+D YHRY ED++L AEMG R S++W+R+FP G+ A NE GL FYD+L +E+ H Sbjct: 58 AIDFYHRYPEDISLFAEMGFNCLRVSIAWARIFPHGDEAQPNEAGLAFYDKLFDEMAKHN 117 Query: 116 IEPIVTLYHWDVPQALMDAYGAWESRRIIDDFDRYAVTLFQRFGDRVKYWVTLNEQNIFI 175 I P+VTL H+++P AL+ YG W +R++I F+RYA T+F+R+ +VK W+T NE N+ + Sbjct: 118 ITPLVTLSHYEMPWALVKNYGGWGNRKVIGFFERYARTVFERYQAKVKLWLTFNEINMSL 177 Query: 176 SLGYRLGLHPPGVKDMKRMYEANHIANLANAKVIQSFRHYVPDGKIGPSFAYSPMYPYDS 235 G+ P +Y+A H +A+A ++ VP+GKIG MYP Sbjct: 178 HAPMT-GVGLPADSSKAEVYQAIHHQLVASALAAKACHDIVPEGKIGNMLLGGLMYPLSC 236 Query: 236 RPENVLAFENAEEFQNHWWM---DVYAWGMYPQAAWNYLESQGLEPTVAPGDWELLQEAK 292 +P+++ FE + QN W DV G YP Y G+ + D L+E Sbjct: 237 KPDDI--FETLQ--QNRSWQFFGDVQCRGAYPGYMLRYFRDNGINLDITDADRAALKETV 292 Query: 293 PDFMGVNYYQTTTVEHNPPDGVSEGVMNTTGKKGTSTSSGIPGLFKTVRNPYVDTTNWDW 352 DF+ +YY T V T ++ + G + V NP++ ++ W W Sbjct: 293 -DFISFSYYMTGCV--------------TADEELNKKARG--NILSMVPNPHLASSEWGW 335 Query: 353 AIDPVGLRIGLRRIANRYRLPILITENGLGEFDTLEPDDIVNDDYRIDYLRRHIQEIQRA 412 IDP+GLR L + +RY+ P+ I ENGLG D +E D +NDDYRI YL H+ +++ A Sbjct: 336 QIDPLGLRTLLNVLWDRYQKPLFIVENGLGAKDKVEADGSINDDYRISYLNDHLVQVREA 395 Query: 413 ITDGVDVLGYCVWSFTDLLSWLNG-YQKRYGFVYVNRDDESEKDLRRIKKKSFYWYQRVI 471 I DGV+++GY W DL+S KRYGF+YV+RDD+ L R +KKSF+WY+ VI Sbjct: 396 IEDGVELMGYTSWGPIDLVSASKAEMSKRYGFIYVDRDDDGNGTLARSRKKSFWWYKEVI 455 Query: 472 ATNGAEL 478 ATNG L Sbjct: 456 ATNGGSL 462 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: 752 Number of extensions: 33 Number of successful extensions: 6 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: 464 Length adjustment: 33 Effective length of query: 445 Effective length of database: 431 Effective search space: 191795 Effective search space used: 191795 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