Align α-glucosidase (PalH) (EC 3.2.1.20) (characterized)
to candidate WP_011385114.1 AMB_RS13755 alpha-glucosidase/alpha-galactosidase
Query= CAZy::AAK28734.1 (464 letters) >NCBI__GCF_000009985.1:WP_011385114.1 Length = 425 Score = 224 bits (572), Expect = 3e-63 Identities = 145/467 (31%), Positives = 226/467 (48%), Gaps = 70/467 (14%) Query: 14 TKIVLVGAGSAQFGYGTLGDIFQSRALYGSEIILHDINPVALAVTEKTAKDFLAKEDLPF 73 TKI +GAGS FG T D+F S L GS ++L D NP ALA + A+ A+ Sbjct: 5 TKIAFLGAGSMSFGLSTFRDMFSSDTLAGSTLVLVDHNPEALARMKALAERMNAEGKAGM 64 Query: 74 IVSATTDRRTALRGAEFVIISIEVGDRFALWDLDWQIPQQYGIQQVYGENGGPGGLFHSL 133 I+ +TTDRR A GA VI S+ + DR LW D++IP++YGI+Q GENGGPGGLF ++ Sbjct: 65 IIESTTDRREAFDGASVVINSVAI-DRMRLWKHDFEIPKKYGIRQTLGENGGPGGLFFTM 123 Query: 134 RIIPPILDICADVADICPDAWIFNYSNPMSRICTTVHRRFPELNFVGMCHEIASLERYLP 193 R +P I +I D+ ++CPDA N+SNP SRI + + P + +G+CH I + Sbjct: 124 RTLPLIFEITRDMEELCPDALFLNFSNPESRIVLALGKYSP-IKSMGLCHGIFMARGAIC 182 Query: 194 EMLNTSFDNLSLRAGGLNHFSVLLDARYKDSGKDAYADVRAKAPDYFASLPGYSDILAYT 253 + + + GLNHF +L R + +G+D Y +RAK P + + +S Sbjct: 183 HITGVPWHDAECWGIGLNHFQWMLQVRNRWTGEDMYPLLRAKEPGFDPTFQPFS------ 236 Query: 254 RQHGKLVDTEGSTERHALGGKDSSYPWADRTLFKEILEKFHCMPITVDSHFGEYISWAGE 313 +++ + P D H GEY+++ E Sbjct: 237 ---------------------------------RKMFNIYGLWPSCSDDHMGEYLAFGWE 263 Query: 314 VSDHRGILDFYTFYRNYLGGVQPKIELK-------------------LKERVVSIMEGIL 354 +H +Y G + ++EL+ + ER +++G++ Sbjct: 264 GGEHG---------HDYAGDARERVELQEAIEGVLAGGPLPDEWKHSVGERTNVVVDGLI 314 Query: 355 TDSGYEEAAVNIPNRGFIKQLPEFIAVEVPAIIDRKGVHGIQV-DIPPGIGGLLSNQIAI 413 + + + + N G I LP +AVEVPAI+D GVH + + +P I L Q + Sbjct: 315 NNRHHYLESAVLMNNGTIPNLPPDLAVEVPAIVDAAGVHPVSLGPLPESIQKLALVQAGV 374 Query: 414 HDLTAEAIIAGSRDLVIQALLVDSVNNQCRAIPELVDVMISRQQPWL 460 L+ EA + S++L +QALL D V N A +L+D + +P++ Sbjct: 375 QQLSVEAAVHASKELALQALLADPVVNSSDAAVKLLDELWEINKPYI 421 Lambda K H 0.321 0.140 0.422 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: 494 Number of extensions: 30 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 464 Length of database: 425 Length adjustment: 32 Effective length of query: 432 Effective length of database: 393 Effective search space: 169776 Effective search space used: 169776 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 (21.9 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