Align 6-phospho-β-glycosidase (GK3214) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate WP_046791705.1 HA49_RS06695 glycoside hydrolase family 1 protein
Query= CAZy::BAD77499.1 (478 letters) >NCBI__GCF_000757425.2:WP_046791705.1 Length = 473 Score = 459 bits (1181), Expect = e-134 Identities = 232/478 (48%), Positives = 314/478 (65%), Gaps = 9/478 (1%) Query: 1 MEHRHLKPFPPGFLWGAASAAYQVEGAWNEDGKGLSVWDVFAKQPGRTFKGTNGDVAVDH 60 M++ LKPFP GFLWGA+++AYQ+EGAWNE+GKG SV D+ + P T T+ VA DH Sbjct: 1 MKYSKLKPFPSGFLWGASTSAYQIEGAWNEEGKGPSVIDMRHEYPQGT---TDFKVASDH 57 Query: 61 YHRYKEDVALMAEMGLKAYRFSVSWSRVFPDGNGAVNEKGLDFYDRLIEELRTHGIEPIV 120 YH+YK+D+ L++E GLKAYRFS++W+R+FP G+G +N GL FY LI+E+R+ G+EPIV Sbjct: 58 YHQYKQDIRLLSETGLKAYRFSIAWTRIFPAGDGEINPAGLQFYHNLIDEIRSCGMEPIV 117 Query: 121 TLYHWDVPQALMDAYGAWESRRIIDDFDRYAVTLFQRFGDRVKYWVTLNEQNIFISLGYR 180 TLYH+D+PQ L D G W +RR +D F RYA TLF G +VKYW+T+NEQN+ I G Sbjct: 118 TLYHFDLPQTLQDI-GGWHNRRTVDAFIRYANTLFTELGSKVKYWLTINEQNLMILQGNA 176 Query: 181 LGLHPPGVKDMKR-MYEANHIANLANAKVIQSFRHYVPDGKIGPSFAYSPMYPYDSRPEN 239 LG P V++ K+ +Y+ NH +A A V+++ P+ IGP+ + +Y +PE+ Sbjct: 177 LGTVDPKVQNNKKHLYQQNHNMLVAQAAVMENLHKNHPEALIGPAPNIALIYAASPKPED 236 Query: 240 VLAFENAEEFQNHWWMDVYAWGMYPQAAWNYLESQGLEPTVAPGDWELLQEAKPDFMGVN 299 VLA EN +N ++D+ G Y AW YLE +G P + GD E+L KPDF+ N Sbjct: 237 VLASENYNAIRNWLYLDMAVSGQYNHLAWAYLEEKGYLPEIEEGDMEILSRGKPDFIAFN 296 Query: 300 YYQTTTVEHNPPDGVSEGVMNTTGKKGTSTSSGIPGLFKTVRNPYVDTTNWDWAIDPVGL 359 YY T TVE + DG E + G K SG G+ + N ++ T + IDPVG Sbjct: 297 YYTTQTVEASRGDGHDEVIRG--GNK--YLKSGEDGVHRGASNNFLPRTEFGTEIDPVGF 352 Query: 360 RIGLRRIANRYRLPILITENGLGEFDTLEPDDIVNDDYRIDYLRRHIQEIQRAITDGVDV 419 R LR I RY LP+LITENG+G FD + D +ND YRIDYLR HI+++Q AITDGV + Sbjct: 353 RNTLRAIYGRYHLPLLITENGIGAFDKPDADGTINDQYRIDYLRSHIEQMQLAITDGVRI 412 Query: 420 LGYCVWSFTDLLSWLNGYQKRYGFVYVNRDDESEKDLRRIKKKSFYWYQRVIATNGAE 477 +GY WS DL+S G KRYG +YVNRD+ +DL+RI+KKS +WY++VI NG + Sbjct: 413 IGYTPWSAIDLISTHQGCSKRYGLIYVNRDEFDLRDLKRIRKKSSFWYEKVILNNGID 470 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: 812 Number of extensions: 43 Number of successful extensions: 5 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: 473 Length adjustment: 33 Effective length of query: 445 Effective length of database: 440 Effective search space: 195800 Effective search space used: 195800 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 24 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