Align Putative alpha-glucosidase AglA (characterized, see rationale)
to candidate SMc01532 SMc01532 alpha-glycosylase
Query= uniprot:I7EUW4 (552 letters) >FitnessBrowser__Smeli:SMc01532 Length = 547 Score = 653 bits (1684), Expect = 0.0 Identities = 306/507 (60%), Positives = 369/507 (72%), Gaps = 6/507 (1%) Query: 15 ADPDWWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVDAIWISPFFTSPMKD 74 +D +WWRGAVIYQ+YPRS+QD++GDG+GDLRG+T+RLPHIASLGVDAIW+SPFFTSP D Sbjct: 7 SDENWWRGAVIYQVYPRSFQDTDGDGMGDLRGVTRRLPHIASLGVDAIWLSPFFTSPQAD 66 Query: 75 FGYDVSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSDQHAWFGESRQSRDN 134 GYDVSDYCDVDPMFG+L++FD+++A AHRLGL+V+ID V+SHTSD+H WF ESR SR N Sbjct: 67 MGYDVSDYCDVDPMFGTLADFDEMLAEAHRLGLKVIIDQVISHTSDRHPWFVESRSSRTN 126 Query: 135 ARADWYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLVSQPDLNFHSPAVQD 194 A+ADWYVWADP+PDGT PNNWLSIFGG W+WD R QYYLHNFL SQPDLNFH+P VQ+ Sbjct: 127 AKADWYVWADPKPDGTAPNNWLSIFGGPGWEWDGVRRQYYLHNFLSSQPDLNFHNPEVQE 186 Query: 195 ALLDVTRFWLERGVDGFRLDTINFYYHDAELRSNPALPPE-QRNATIAPSVNPYNHQEHL 253 A+L RFWL+RGVDGFRLDT NFY+HD LR NP L P+ + AP VNPY Q+HL Sbjct: 187 AVLATVRFWLDRGVDGFRLDTANFYFHDRLLRDNPPLVPDPDATSRDAPEVNPYGMQDHL 246 Query: 254 YSKNQPENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGSYTAANTGVHMCYAFELL 313 Y K QPENL FL RFRA+LDEY +A VGEVGD R L+ + +YT+ +HMCY F+LL Sbjct: 247 YDKTQPENLDFLRRFRAVLDEYGGRATVGEVGDGSRSLQTVAAYTSGGDKLHMCYTFDLL 306 Query: 314 AKDVLTASRLAEVFAEVDRVAANGWACWAFSNHDVIRHSSRWGLNPA----AQRLFTTMM 369 + TA +GW CWAFSNHDV+RH SR+ L A +L +++ Sbjct: 307 GPE-FTARHFRRCVENFQSTVTDGWVCWAFSNHDVMRHVSRFALREADRERVAKLAISLL 365 Query: 370 MCLRGTTCIYQGEELGLPEADIAFEDLQDPYGIEFWPEFKGRDGCRTPMVWEPSNGSGGF 429 LRGT C+YQGEELGLPEA++AFE+L+DPYGI FWP F GRDGCRTPMVWE + GF Sbjct: 366 ASLRGTICLYQGEELGLPEAELAFEELRDPYGIRFWPAFAGRDGCRTPMVWERELSNAGF 425 Query: 430 SAGKPWLPVSPEHLNLSVASQEADPDAMLHHYRRAIALRKAHPALAVGTHDQLRAEGNVA 489 SAG PWLPV H L+V +QE A+L HYR+ + R+A AL G L ++ Sbjct: 426 SAGTPWLPVRDGHRMLAVDAQEGVEGAVLEHYRQTLGFRRAQSALVDGDMVFLGTNQDLL 485 Query: 490 FFTRQDRDEVIFCAFNLGDIPAEITLP 516 FTR+ DE + FNL P LP Sbjct: 486 VFTREKDDERLLFVFNLTQEPQTFHLP 512 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: 1069 Number of extensions: 48 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