Align 6-phospho-β-glycosidase (GK1856) (EC 3.2.1.85|3.2.1.86) (characterized)
to candidate WP_011382666.1 AMB_RS01115 beta-glucosidase
Query= CAZy::BAD76141.1 (470 letters) >NCBI__GCF_000009985.1:WP_011382666.1 Length = 453 Score = 294 bits (753), Expect = 4e-84 Identities = 169/451 (37%), Positives = 245/451 (54%), Gaps = 24/451 (5%) Query: 12 RFPAGFWWGSATSATQIEGAANEGGKGKNIWDHWYEQEPHRFFQGVGPEVASDFYHRYKE 71 +FP F+WG++T+A QIEGA + G+G IWD + + G +VA D YHRY E Sbjct: 16 QFPKDFFWGASTAAYQIEGAYDTDGRGMTIWDKFTADG--KIMDGSSAKVACDHYHRYPE 73 Query: 72 DIALMKEIGHNSFRFSISWSRLIPDGVGEVNPEAVRFYNAVIDELLANGIEPFVNLYHFD 131 DIALMK G N++RFS++W R+IP G G +N + + FY+ ++D++L GI+P LYH+D Sbjct: 74 DIALMKAAGFNAYRFSLAWPRIIPAGTGAINAKGLDFYDRLVDKILEAGIKPMACLYHWD 133 Query: 132 MPLAMQTIGGWENREVVDAYARYASLCFQLFGDRVKTWFTHNEPIVPVEGGYLYDFHYPN 191 +P ++ GGW+ R++V +A YA + + GDRVK W+ NEP V GY H P Sbjct: 134 LPQPLEDKGGWQGRDIVGPFAEYARIATKRLGDRVKDWYMLNEPNVVAIIGYGIGEHAPG 193 Query: 192 V-VDFRRAVQVAYHTMIAHAKAVAAFRRAAIPDGKIGIILNLTPSYPRSQHPADVKAAHI 250 + ++ +H +A A+ A RA D +G ++NL P + P + AA Sbjct: 194 YKLGEDGILKALHHQNLAQGTALRAI-RAEHSDAVLGTVINLQPCRSQDDDPKNRAAAIR 252 Query: 251 ADLLFNRSFLDPAVKGEYPQDLIELLDEYGFLPVTKANDRELIKENTIDLLGINYYQPRR 310 D ++NR LD ++G P L E + + K D E IK ID+LGINYY Sbjct: 253 WDAVWNRVPLDGVMRGAIPDVLAEKMAH-----IVKPGDMETIK-FPIDMLGINYYSRMT 306 Query: 311 VKAKENMPNPDAPFLPERFFDYYAMPGRKMNPYRGWEIYEKGIYDILINIKENYGNIECF 370 +K +E +P F + D + W + G+YD+L KE YGN F Sbjct: 307 MKHEEG--HPFDVFWGDAHCDRWTA--------MAWPVQPDGLYDLLREFKELYGNPAVF 356 Query: 371 ISENGMGVEGEERFRDESGMIHDDYRIEFIREHLKWVHRAIEEGVNVKGYHLWTFMDNWS 430 I+ENG + G +HD R+ FIR+H+ V RA+++G NVKGY +W+ +DN+ Sbjct: 357 IAENGAAYDD---VVTPDGQVHDAERVAFIRDHVSEVARAVKDGCNVKGYLVWSLLDNFE 413 Query: 431 WTNAYKNRYGLVAVDLENGLKRTIKKSGYWF 461 W R+G+V VD E LKRT K S WF Sbjct: 414 WAYGLSKRFGIVRVDYET-LKRTPKDSYKWF 443 Lambda K H 0.321 0.140 0.446 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: 710 Number of extensions: 45 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: 470 Length of database: 453 Length adjustment: 33 Effective length of query: 437 Effective length of database: 420 Effective search space: 183540 Effective search space used: 183540 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