Align 6-P-α-glucosidase (MalH) (EC 3.2.1.122) (characterized)
to candidate BWI76_RS18685 BWI76_RS18685 6-phospho-alpha-glucosidase
Query= CAZy::AAB63015.1 (441 letters) >FitnessBrowser__Koxy:BWI76_RS18685 Length = 442 Score = 640 bits (1650), Expect = 0.0 Identities = 298/439 (67%), Positives = 363/439 (82%) Query: 3 QFSILIAGGGSTFTPGIILMLLDNLDKFPIRQIKMFDNDAERQAKIGEACAILLKEKAPQ 62 +F + IAGGGST+TPGI++MLL+N+D+FP+ +I+++DN +RQ+ IGEACAIL+ E+ PQ Sbjct: 4 KFVVTIAGGGSTYTPGIVMMLLENMDRFPLSEIRLYDNHRDRQSVIGEACAILVAERYPQ 63 Query: 63 IKFSYSTNPEEAFTDIDFVMAHIRVGKYPMRELDEKIPLRHGVVGQETCGPGGIAYGMRS 122 + FS++T+P+EAFT +DFVMAHIRVG Y MRE DEKIPL+HGV+GQETCGPGGIAYGMRS Sbjct: 64 VAFSFTTDPQEAFTGVDFVMAHIRVGLYEMREKDEKIPLKHGVIGQETCGPGGIAYGMRS 123 Query: 123 IGGVIGLIDYMEKYSPNAWMLNYSNPAAIVAEATRRLRPNSKVLNICDMPIGIEVRMAEI 182 I GV+ L+DYME YSP AWMLNYSNPAAIVAEATRRLRP +K++NICDMP+ IE A+I Sbjct: 124 IAGVLELVDYMETYSPGAWMLNYSNPAAIVAEATRRLRPTAKIINICDMPVAIEGLFADI 183 Query: 183 LGLESRKDMDIMYYGLNHFGWWKSVRDKQGNDLMPKLREHVSQYGYVVPKGDNQHTEASW 242 LGL+SRK+M++ Y+GLNHFGWW S+ DK GNDLMP L+ HV++ GY PK D QH SW Sbjct: 184 LGLKSRKEMNVRYFGLNHFGWWTSITDKAGNDLMPALKNHVAELGYCSPKEDFQHKAPSW 243 Query: 243 NDTFAKAKDVLALDPTTLPNTYLKYYLFPDYVVEHSNKEYTRANEVMDGREKFVFGECEK 302 +TF K KDV ALD TLPNTYLKYY + DY V HS+ ++TRANEV+ GREK VF + Sbjct: 244 IETFKKVKDVFALDTDTLPNTYLKYYFYADYEVAHSDPDFTRANEVIAGREKEVFDMARE 303 Query: 303 VVKNQSSEGCALHIDEHASYIVDLARAIAFNTKEKMLLIVENNGAIVNFDSTAMVEIPCI 362 +V QS + H HA++IVDLA AIAFNT+E+MLLIVENNGAI NFD TAMVE+PC+ Sbjct: 304 IVARQSGKAAHFHAGAHATFIVDLACAIAFNTQERMLLIVENNGAIANFDDTAMVEVPCL 363 Query: 363 VGSNGPEPLVVGRIPQFQKGMMEQQVTVEKLTVEAWIEGSYQKLWQAITMSKTVPSAKVA 422 VG NGPEPL +G+IP FQKGMMEQQV VEKL V+AW+EGSYQKLWQA+T+SKTVPSA VA Sbjct: 364 VGVNGPEPLAMGKIPLFQKGMMEQQVAVEKLVVDAWVEGSYQKLWQAMTLSKTVPSASVA 423 Query: 423 KDILDDLIEANKEYWPVLK 441 K ILD+LI AN+ YWP L+ Sbjct: 424 KAILDELIVANRGYWPELR 442 Lambda K H 0.319 0.136 0.407 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: 634 Number of extensions: 24 Number of successful extensions: 1 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: 441 Length of database: 442 Length adjustment: 32 Effective length of query: 409 Effective length of database: 410 Effective search space: 167690 Effective search space used: 167690 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