Align Probable alpha-glucosidase; EC 3.2.1.20 (uncharacterized)
to candidate GFF2114 Psest_2157 trehalose synthase
Query= curated2:Q9Z3R8 (551 letters) >FitnessBrowser__psRCH2:GFF2114 Length = 1108 Score = 259 bits (663), Expect = 3e-73 Identities = 199/597 (33%), Positives = 286/597 (47%), Gaps = 112/597 (18%) Query: 17 WWRGAVIYQIYPRSFQDTNGDGIGDLQGITARLPHIAGLGADAIWISPFFTSPMRDFGYD 76 W++ AV+YQ++ +SF D+N DG+GD G+ +L +IA LG + IW+ PF+ SP RD GYD Sbjct: 16 WYKDAVVYQVHLKSFYDSNNDGVGDFAGLIDKLDYIADLGVNTIWLLPFYPSPRRDDGYD 75 Query: 77 VSNYVDVDPIFGTLEDFDALIAEAHRLGLRVMIDLVLSHTSDRHPWFVESRSSRSNAKA- 135 +++Y V P +GT+ D IAEAH+ GLRV+ +LV++HTSD+HPWF +R +R + A Sbjct: 76 IADYRGVHPEYGTMADARRFIAEAHKRGLRVITELVINHTSDQHPWFQRARKARKGSAAR 135 Query: 136 DWYVWADS--KPDGTPPNNWLSIF---GGSAWQWDPTRLQYYLHNFLTSQPDLNLHNPQV 190 ++YVW+D+ K DGT IF S W WDP QY+ H F + QPDLN NPQV Sbjct: 136 NFYVWSDTDEKYDGT-----RIIFLDTEKSNWTWDPVAKQYFWHRFYSHQPDLNFDNPQV 190 Query: 191 QEALLAVERFWLERGVDGFRLDTINFYFHDRELRDNPALVPERRNASTAPAVNPYNYQEH 250 +A+LAV R+WL+ G+DG RLD I Y +R+ +N Sbjct: 191 MKAVLAVMRYWLDMGIDGLRLDAIP-YLVERDGTNN------------------------ 225 Query: 251 IYDKNRPENLEFLKRFRAVMD-EFPAIAAVGEVGD--SQRGLEIAGEYTSGGDKVHMCYA 307 +N PE LK RA +D +P + E L GE GD+ HM + Sbjct: 226 ---ENLPETHAVLKAIRAEIDANYPDRMLLAEANQWPEDTQLYFGGEDGGPGDECHMAFH 282 Query: 308 FEFLAPDRLT-PQRVAEVLRDFHRAAPE-----GWACWAFSNHD-----VVRHVSR---W 353 F + + Q + D R P+ WA + NHD +V R W Sbjct: 283 FPLMPRMYMAIAQEDRFPITDILRQTPDIPENCQWAIF-LRNHDELTLEMVTDRERDYLW 341 Query: 354 ADGVTDHDA-------------------HAKLLASLLMSLRGTVCIYQGEELALAEAELD 394 +D A +LL SLL+S+ GT IY G+E+ + D Sbjct: 342 NYYASDKRARINLGIRRRLAPLLERDRRRIELLNSLLLSMPGTPVIYYGDEIGMG----D 397 Query: 395 YEDLQDPYGIQFWPDFKGRDGCRTPMVWESLPDGGFSSATP----WLPISQ---SHIPRA 447 L D RDG RTPM W +GGFS A P P+ + Sbjct: 398 NIFLGD------------RDGVRTPMQWSVDRNGGFSRADPPNLVLPPVMDPLYGYYTIN 445 Query: 448 VAVQEGDPASVLHHYRRFLAFRKANPALAKGEIEFV-ETRGSLLGFLR-----SHGNEKV 501 V Q+ DP S+L+ RR L RK A +G ++ + + +L +LR + E + Sbjct: 446 VEAQQRDPHSLLNWTRRMLTIRKQFKAFGRGTLKMLAPSNRRILAYLREFTGANGDTEII 505 Query: 502 FCLFNMSDEAATKELPMKR------LEPLEGHGFVS-EILDHEVKLPAWGAFFARLA 551 FC+ N+S A EL M + +E + G F L + + LP +G ++ +LA Sbjct: 506 FCVANVSRSAQAAELEMSQYAGMVPVEMVGGSAFPPIGQLPYLLTLPPYGFYWFQLA 562 Lambda K H 0.321 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: 1578 Number of extensions: 89 Number of successful extensions: 5 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: 551 Length of database: 1108 Length adjustment: 41 Effective length of query: 510 Effective length of database: 1067 Effective search space: 544170 Effective search space used: 544170 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: 55 (25.8 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