Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate PP_4059 PP_4059 fused trehalose synthase B/maltokinase
Query= uniprot:A8LLL3 (552 letters) >FitnessBrowser__Putida:PP_4059 Length = 1106 Score = 235 bits (599), Expect = 8e-66 Identities = 181/559 (32%), Positives = 264/559 (47%), Gaps = 74/559 (13%) Query: 16 DPDWWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKDF 75 DP W++ AVIYQ++ +SF DSN DGIGD G++ ++ YIA LGV+ +W+ PF+ SP +D Sbjct: 13 DPLWYKDAVIYQLHIKSFFDSNNDGIGDFAGLISKLDYIAELGVNTLWLLPFYPSPRRDD 72 Query: 76 GYDISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDNP 135 GYDI++Y V P +GS+AD I AH GLRV+ +LV++HTSDQHPWF+ +R ++ Sbjct: 73 GYDIAEYKAVHPDYGSMADARRFIAEAHKRGLRVITELVINHTSDQHPWFQRARHAKRGS 132 Query: 136 KA-DWYVWA--DAKPDGTPPNNWLSIF---GGSGWHWDARRCQYYLHNFLTSQPDLNFHC 189 KA ++YVW+ D K DGT IF S W WD QY+ H F + QPDLNF Sbjct: 133 KAREFYVWSDDDQKYDGT-----RIIFLDTEKSNWTWDPVAGQYFWHRFYSHQPDLNFDN 187 Query: 190 ADVQDALLGVGRFWLDRGVDGFRLDTINFYV-------------HDAELRDNPPLPPEER 236 V A++GV RFWLD GVDG RLD I + + HD + Sbjct: 188 PQVLKAVIGVMRFWLDLGVDGLRLDAIPYLIERDGTNNENLAETHDVLKAIRAEIDANYP 247 Query: 237 NSNIAPEVNPY-NHQRHLYSKNQPENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILG 295 + + E N + R + + + F M Y A+A + D +IL Sbjct: 248 DRMLLAEANQWPEDTRPYFGEGDGDECHMAFHFPLMPRMYMALA----MEDRFPITDILR 303 Query: 296 QYTRGETGVHMCYAFEFLAQEKLTAKRVAEVLNKVDEVASDGWACWAFSNHDVMRHVSRW 355 Q E + +A ++LT + V D W +A + R Sbjct: 304 Q--TPEIPANCQWAIFLRNHDELTLEMV------TDRERDYLWNYYAEDRRARINLGIRR 355 Query: 356 DLTPGAQRG------MLTLLMCLRGSVCLYQGEELGLPEAEVAFDDLQDPYGIEFWPEYK 409 L P QR + +LL+ + G+ LY G+ELG+ + D Sbjct: 356 RLAPLLQRDRRRIELLTSLLLSMPGTPTLYYGDELGMGDNIYLGD--------------- 400 Query: 410 GRDGCRTPMVWQSDNMSGGFSIHRPW---LPVSTEHL----GLAVAVQEEAPDALLHHYR 462 RDG RTPM W D +GGFS P LP + L + V Q P +LL+ R Sbjct: 401 -RDGVRTPMQWSPDR-NGGFSRADPQRLVLPPIMDPLYGYQTVNVEAQSHDPHSLLNWTR 458 Query: 463 RALAFRRAHPALVKGDISDVTVVG-DVISFLRKDPE-----ETVFVAINMSDAPGAVDLP 516 R LA R+ A +G + +T +++++R+ + E + N+S A A +L Sbjct: 459 RMLAVRKQQKAFGRGSLRTLTPSNRRILAYIREYTDADGNTEVILCVANVSRAAQAAELE 518 Query: 517 PGNWM-QIGAELNSGGTSP 534 + ++ E+ G P Sbjct: 519 LSQYADKVPVEMLGGSAFP 537 Lambda K H 0.321 0.138 0.451 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: 1619 Number of extensions: 79 Number of successful extensions: 4 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: 552 Length of database: 1106 Length adjustment: 41 Effective length of query: 511 Effective length of database: 1065 Effective search space: 544215 Effective search space used: 544215 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: 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