Align Putative alpha-glucosidase AglA (characterized, see rationale)
to candidate CCNA_02368 CCNA_02368 alpha-glucosidase
Query= uniprot:I7EUW4 (552 letters) >FitnessBrowser__Caulo:CCNA_02368 Length = 547 Score = 536 bits (1381), Expect = e-157 Identities = 264/513 (51%), Positives = 334/513 (65%), Gaps = 10/513 (1%) Query: 9 PAQVLAADPDWWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVDAIWISPFF 68 P + + +WWRGAVIYQ+YPRS+ DSNGDG+GDL GIT L HIASLGV+ +W+SPFF Sbjct: 16 PDAETSMNAEWWRGAVIYQVYPRSFADSNGDGVGDLPGITAHLDHIASLGVEGVWLSPFF 75 Query: 69 TSPMKDFGYDVSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSDQHAWFGES 128 TSPMKDFGYDVS+YCDVDP+FG+L++FD L+A AH LGL+++IDLV SHTSD+H WF ES Sbjct: 76 TSPMKDFGYDVSNYCDVDPIFGTLADFDALIARAHALGLKIIIDLVFSHTSDEHPWFVES 135 Query: 129 RQSRDNARADWYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLVSQPDLNFH 188 RQ R NA+ADW+VWAD +PDG+PP+NW S+FGG AW WD RR QYY+HNFL SQP LN H Sbjct: 136 RQDRSNAKADWFVWADAKPDGSPPSNWQSVFGGPAWTWDARRGQYYMHNFLSSQPQLNLH 195 Query: 189 SPAVQDALLDVTRFWLERGVDGFRLDTINFYYHDAELRSNPALPPEQRNATIAPSVNPYN 248 +PAVQ+ALL VT+FW+++GVDGFR D INF HD L NP LPP + P++ Sbjct: 196 NPAVQEALLAVTQFWIDKGVDGFRFDAINFSMHDPALTDNPPLPPGGKR------TRPFD 249 Query: 249 HQEHLYSKNQPENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGSYTAANTGVHMCY 308 Q+ +++++ + FL R RAL D + +V EVG E M +TA ++ Y Sbjct: 250 FQDKIHNQSHADIPKFLSRLRALTDAAGGRFSVAEVGGDHAERE-MKLFTAGEDRLNSAY 308 Query: 309 AFELLAKDVLTASRLAEVFAEVDRVAANGWACWAFSNHDVIRHSSRWGL---NPAAQRLF 365 F L D L + + A A GW W FSNHD R SRW A L Sbjct: 309 GFLYLYADKLIGEMIPQGAAMWPGEAGEGWPSWTFSNHDAPRAVSRWAEGRDRKAFAELC 368 Query: 366 TTMMMCLRGTTCIYQGEELGLPEADIAFEDLQDPYGIEFWPEFKGRDGCRTPMVWEPSNG 425 ++M LRG +YQGEELGLP+A + FE LQDP I WP+ GRDG RTPM W Sbjct: 369 LLLLMGLRGNVFVYQGEELGLPQAHVPFERLQDPEAIANWPQTLGRDGARTPMPWVSGAL 428 Query: 426 SGGFSAGKPWLPVSPEHLNLSVASQEADPDAMLHHYRRAIALRKAHPALAVGTHDQLRAE 485 + GFS +PWLPV PEHL L+V +QEADP + L+ RR I LR+A+PAL G + Sbjct: 429 NAGFSGVEPWLPVDPEHLPLAVDAQEADPASTLNVARRLIGLRRAYPALRTGAITFIDTN 488 Query: 486 GNVAFFTRQDRDEVIFCAFNLGDIPAEITLPEG 518 + F R + + + AFNLG +LP+G Sbjct: 489 SPLLIFQRGEGADAVLLAFNLGFETVTWSLPDG 521 Lambda K H 0.321 0.137 0.444 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: 1057 Number of extensions: 51 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: 552 Length of database: 547 Length adjustment: 36 Effective length of query: 516 Effective length of database: 511 Effective search space: 263676 Effective search space used: 263676 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: 53 (25.0 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