Align alpha,alpha-trehalose phosphorylase (EC 2.4.1.64) (characterized)
to candidate 15436 b1316 predicted hydrolase (NCBI)
Query= BRENDA::D6XSD4 (757 letters) >FitnessBrowser__Keio:15436 Length = 755 Score = 307 bits (786), Expect = 2e-87 Identities = 233/777 (29%), Positives = 367/777 (47%), Gaps = 81/777 (10%) Query: 5 ISSKALDQDQLLVDESLFAQGNGYLGIRGNFEEGYAADMTTIRGAYL-NAFHDVVPIEYG 63 +S Q L SL AQGNGYLG+R + EE Y RG YL +H E Sbjct: 7 LSEPHFSQHTLNKYASLMAQGNGYLGLRASHEEDYTRQT---RGMYLAGLYHRAGKGEIN 63 Query: 64 EKLFGFPDTQQKLVNNIDVQSIRIIIDGDDFSLFQGEILDFERFLYMKDGYSERRIHWKS 123 E LVN DV + I I+G+ FSL ++R L G R + W++ Sbjct: 64 E-----------LVNLPDVVGMEIAINGEVFSLSHEA---WQRELDFASGELRRNVVWRT 109 Query: 124 PAGKEVSIHFYRMISFTDKELFVQWIDIEPISQVQEIEIVSTVDGDVSNFVEASDPRVAS 183 G +I R +S L I I P+ D D S + + Sbjct: 110 SNGSGYTIASRRFVSADQLPLIALEITITPL------------DADASVLISTGIDATQT 157 Query: 184 GHAKR-LHVTDVQDKGPY-MQVSDETEVSKLKVSATTWVSASREALKESRSSFEGKVEER 241 H ++ L T V+ G + MQ S T+ + V+ + S + + + ++ Sbjct: 158 NHGRQHLDETQVRVFGQHLMQGSYTTQDGRSDVAISCCCKVSGDVQQCYTAKERRLLQHT 217 Query: 242 RTFSGEGSLRYEKRSVYTDTYRHESSPS-----EAGFELAKRLSAVSLDELIRGQRAYLN 296 G ++ V+ D +R + + A + + S D+L+ Sbjct: 218 SAQLHAGETMTLQKLVWID-WRDDRQAALDEWGSASLRQLEMCAQQSYDQLLAASTENWR 276 Query: 297 RFWQTSDIRIAGDDKL-QEGIRFNLYQL-LQSVGKEPTSNISAKGLSGEGYEGHYFWDTE 354 ++WQ I + G + Q+ + + LY L + + + S+I+AKGL+GEGY+GH FWDTE Sbjct: 277 QWWQKRRITVNGGEAHDQQALDYALYHLRIMTPAHDERSSIAAKGLTGEGYKGHVFWDTE 336 Query: 355 IYMYPPFLMTDPEIAKNLLLHRFSLLDAARERAKEMGHRQGALFPWRTI-SGGECSAFFP 413 +++ P L +DP +A++LL +R+ L A+E+A+ G QGALFPW + SG E + F Sbjct: 337 VFLLPFHLFSDPTVARSLLRYRWHNLPGAQEKARRNGW-QGALFPWESARSGEEETPEFA 395 Query: 414 A-------------GSAQYHISADIAYSFIQYYLTTGDEVFLADYGAELLVETARLWIDT 460 A A++H+ ADIA++ IQY+ TTGDE F+A G LL+ETA+ WI Sbjct: 396 AINIRTGLRQKVASAQAEHHLVADIAWAVIQYWQTTGDESFIAHEGMALLLETAKFWISR 455 Query: 461 GHMKDGRFRIDDVTGPDEYTCIVNNNYYTNSMAKHNLEWAVKAMALVEERHPTVYKNLAA 520 + R I DV GPDEYT VNNN YT+ MA++N++ A+ N+A Sbjct: 456 AVRVNDRLEIHDVIGPDEYTEHVNNNAYTSYMARYNVQQAL---------------NIAR 500 Query: 521 RLAVTDDELKAFREASE----SMYYPYSDSHRIHAQDDTFLNKQVWDIEG--TPKEEFPL 574 + +DD AF +E ++ P + QDD+F+ K ++ + + Sbjct: 501 QFGCSDD---AFIHRAEMFLKELWMPEIQPDGVLPQDDSFMAKPAINLAKYKAAAGKQTI 557 Query: 575 LLHYHPLTLYRYQVCKQADTVLSHFLLEDEADEETIRRSYDYYEQVTTHDSSLSFCVFSI 634 LL Y + Q+ KQAD V+ +++L ++ + + +YE T HDSSLS + I Sbjct: 558 LLDYSRAEVNEMQILKQADVVMLNYMLPEQFSAASCLANLQFYEPRTIHDSSLSKAIHGI 617 Query: 635 MAAKLGYEKKAYEYFSETARLDLDNTHKNTKDGLHMANMGGTWLALVSGFGGMRVKETGL 694 +AA+ G ++Y+++ E +DL + DG+H A G WL + GF G+ V++ L Sbjct: 618 VAARCGLLTQSYQFWREGTEIDLGADPHSCDDGIHAAATGAIWLGAIQGFAGVSVRDGEL 677 Query: 695 HFAPRLPEAWDSLSFQIQYQGRVIALDIGRDKTVYTLTEGDVINMYHHGKLFTLTEQ 751 H P LPE W LSF + +QG L + D + +++ +G+L T+ E+ Sbjct: 678 HLNPALPEQWQQLSFPLFWQG--CELQVTLDAQRIAIRTSAPVSLRLNGQLITVAEE 732 Lambda K H 0.319 0.135 0.401 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: 1319 Number of extensions: 60 Number of successful extensions: 6 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: 757 Length of database: 755 Length adjustment: 40 Effective length of query: 717 Effective length of database: 715 Effective search space: 512655 Effective search space used: 512655 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: 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