Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate CCNA_02368 CCNA_02368 alpha-glucosidase
Query= uniprot:H3K096 (538 letters) >FitnessBrowser__Caulo:CCNA_02368 Length = 547 Score = 556 bits (1434), Expect = e-163 Identities = 269/506 (53%), Positives = 345/506 (68%), Gaps = 14/506 (2%) Query: 4 NMMWWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDF 63 N WWRG VIYQ+YPRSF DS GDGVGDL GIT LD++ASL V+G+WLSPFFTSPM DF Sbjct: 23 NAEWWRGAVIYQVYPRSFADSNGDGVGDLPGITAHLDHIASLGVEGVWLSPFFTSPMKDF 82 Query: 64 GYDVSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNP 123 GYDVS+Y DVDP+FGTL DF AL+ +AH+LGLK++ID V SHTSD+HPWF ESRQ+R+N Sbjct: 83 GYDVSNYCDVDPIFGTLADFDALIARAHALGLKIIIDLVFSHTSDEHPWFVESRQDRSNA 142 Query: 124 KADWFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQA 183 KADWFVWAD KPDG+PP+NW S+FGG AWT+D+RR QYY+HNFL+SQP +N H+P ++A Sbjct: 143 KADWFVWADAKPDGSPPSNWQSVFGGPAWTWDARRGQYYMHNFLSSQPQLNLHNPAVQEA 202 Query: 184 QLDNMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYD 243 L +FW+D GVDGFR D +NF HD L DNPP+P G +T P+ +Q +++ Sbjct: 203 LLAVTQFWIDKGVDGFRFDAINFSMHDPALTDNPPLPPGGKRT------RPFDFQDKIHN 256 Query: 244 LSRPENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNMP 303 S + FL LRAL D G +V E+G D+ M +TAG D+L+ AY F L Sbjct: 257 QSHADIPKFLSRLRALTDAAGGRFSVAEVGGDHAEREMKLFTAGEDRLNSAYGFLYL--- 313 Query: 304 HSASYLREVIERFQRL----AGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLF 359 ++ + E+I + + AG+ WP W SNHD R+ +RW D A+ ++ L +L Sbjct: 314 YADKLIGEMIPQGAAMWPGEAGEGWPSWTFSNHDAPRAVSRWAEGRDRKAFAELCLLLLM 373 Query: 360 SLRGSVCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPWTDGE-QGGFS 418 LRG+V +YQGEELGLP+A VPFER+QDP WP+ GRDG RTPMPW G GFS Sbjct: 374 GLRGNVFVYQGEELGLPQAHVPFERLQDPEAIANWPQTLGRDGARTPMPWVSGALNAGFS 433 Query: 419 PVEPWLPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLG 478 VEPWLP++ HL LAV Q+ DP +TLN R L+ RR++PAL G ++ +D LL Sbjct: 434 GVEPWLPVDPEHLPLAVDAQEADPASTLNVARRLIGLRRAYPALRTGAITFIDTNSPLLI 493 Query: 479 FTRQKGDETLLCVFNLTGQEQQTTLP 504 F R +G + +L FNL + +LP Sbjct: 494 FQRGEGADAVLLAFNLGFETVTWSLP 519 Lambda K H 0.320 0.138 0.443 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: 997 Number of extensions: 50 Number of successful extensions: 4 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: 538 Length of database: 547 Length adjustment: 35 Effective length of query: 503 Effective length of database: 512 Effective search space: 257536 Effective search space used: 257536 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: 52 (24.6 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