Align 6-phospho-α-glucosidase (Pagl;CAC3426) (EC 3.2.1.122) (characterized)
to candidate 15852 b1734 cryptic phospho-beta-glucosidase, NAD(P)-binding (NCBI)
Query= CAZy::AAK81356.1 (445 letters) >FitnessBrowser__Keio:15852 Length = 450 Score = 165 bits (417), Expect = 3e-45 Identities = 134/454 (29%), Positives = 214/454 (47%), Gaps = 40/454 (8%) Query: 2 KKYSICIVGGGSRYTPDMLAMLCNQKERFPLRKIVLYDNESER----------QETVGNY 51 +K + +GGGS YTP++L + P+ ++ L D E + Q + N Sbjct: 3 QKLKVVTIGGGSSYTPELLEGFIKRYHELPVSELWLVDVEGGKPKLDIIFDLCQRMIDN- 61 Query: 52 AKILFKEYYPELEEVIWTTDEKEAFEDIDFALMQIRAGRLKMREKDEKISLKHGCLGQET 111 A + K Y T D +EA +D DF Q+R G+L RE DE+I L HG LGQET Sbjct: 62 AGVPMKLYK--------TLDRREALKDADFVTTQLRVGQLPARELDERIPLSHGYLGQET 113 Query: 112 CGAGGFAYGLRSVPAVIDLIKSIRTYSPKCWILNYSNPAAIVAEATKRVFPNDYRIINIC 171 GAGG GLR++P + D++K + P W++N++NPA +V EA R R I +C Sbjct: 114 NGAGGLFKGLRTIPVIFDIVKDVEELCPNAWVINFTNPAGMVTEAVYR-HTGFKRFIGVC 172 Query: 172 DMPIAIMDIYAAVLGLK-RRDLEPKYFGLNHFGWFTHILDKKTGENYLPKLREILKTPVD 230 ++PI + VL LK DL FGLNH + +L N + E+L D Sbjct: 173 NIPIGMKMFIRDVLMLKDSDDLSIDLFGLNHMVFIKDVL-----INGKSRFAELL----D 223 Query: 231 VQTEPLFQEKSWKSTFE--FMSQMINDYDEYLPNTYLQYYLYPAKMRNKENPEYTRAN-- 286 + S K+ F+ F +I + LP +YL YY +M E EY + Sbjct: 224 GVASGQLKASSVKNIFDLPFSEGLIRSLN-LLPCSYLLYYFKQKEMLAIEMGEYYKGGAR 282 Query: 287 -EVMDGNEKETYERMHKIISLGKIHGTKYELTSDVGCHAEYIVDLATAIANNTNEIFLII 345 +V+ EK+ +E ++K L K+ + E +++ ++ AI N+ + Sbjct: 283 AQVVQKVEKQLFE-LYKNPEL-KVKPKELEQRGG-AYYSDAACEVINAIYNDKQAEHYVN 339 Query: 346 TENKGTINNVSKDMMVEVPCRVGSNGVEPLV-VGSIPAFYKGLMENQYAYEKLSVDACLE 404 + G I+N+ D VE+ C++G +G P + GL+ +E + +A L Sbjct: 340 IPHHGQIDNIPADWAVEMTCKLGRDGATPHPRITHFDDKVMGLIHTIKGFEIAASNAALS 399 Query: 405 GSYQKALQALVLNRTVVNTDVAKELLKDLIEANK 438 G + L AL L+ V + A+ L +++I A++ Sbjct: 400 GEFNDVLLALNLSPLVHSDRDAELLAREMILAHE 433 Lambda K H 0.319 0.136 0.406 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: 475 Number of extensions: 26 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: 445 Length of database: 450 Length adjustment: 33 Effective length of query: 412 Effective length of database: 417 Effective search space: 171804 Effective search space used: 171804 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 (21.7 bits) S2: 51 (24.3 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