Align alpha,alpha-trehalase (EC 3.2.1.28) (characterized)
to candidate H281DRAFT_02882 H281DRAFT_02882 alpha,alpha-trehalase
Query= BRENDA::P13482 (565 letters) >FitnessBrowser__Burk376:H281DRAFT_02882 Length = 627 Score = 506 bits (1304), Expect = e-148 Identities = 262/546 (47%), Positives = 340/546 (62%), Gaps = 13/546 (2%) Query: 31 EETPVTPQPPDILLGPLFNDVQNAKLFPDQKTFADAVPNSDPLMILADYRMQQNQSGFDL 90 + +PV P PP L+ DVQ A L+PD KTFAD VP + P I A Y + Q GF+L Sbjct: 79 QASPVVPVPPSEQYPDLYRDVQLAHLYPDSKTFADMVPLAPPAQIAAAYETARQQPGFNL 138 Query: 91 RHFVNVNFTLP-KEGEKYVPPEGQSLREHIDGLWPVLTRSTENTEK-WDSLLPLPEPYVV 148 FV NFTLP + + YV + + HID LW VL R + W SLLPLP+ Y+V Sbjct: 139 GDFVKRNFTLPVRMSKSYVSDPNEDVVSHIDTLWNVLRREPDAAASPWSSLLPLPDAYIV 198 Query: 149 PGGRFREVYYWDSYFTMLGLAESGHWDKVADMVANFAHEIDTYGHIPNGNRSYYLSRSQP 208 PG RF E+YYWDSYF MLGL SGH V D + NFA I+ YGHIPNGNR+YYLSRSQP Sbjct: 199 PGDRFDEIYYWDSYFIMLGLEASGHHAWVVDELKNFATLINRYGHIPNGNRTYYLSRSQP 258 Query: 209 PFFALMVELLAQHEGDAALKQYLPQMQKEYAYWMDGVENLQAGQQEKRVVKLQDGTLLNR 268 PFFA MV L+A+ +GDA QYLP++Q+EYAYWMDG E L AG + VV+L DG+LLNR Sbjct: 259 PFFAQMVRLVAEKDGDAVYAQYLPELQREYAYWMDGSEGLPAGHANRHVVRLADGSLLNR 318 Query: 269 YWDDRDTPRPESWVEDIATAKSNPNRPATEIYRDLRSAAASGWDFSSRWMDNPQQLNTLR 328 YWD+R PR ES+ EDIAT++ P R A +++R+LR+ +GWDFSSRW + + L T+ Sbjct: 319 YWDERAAPRDESYREDIATSQQTPQRNADDLWRNLRAGGETGWDFSSRWFADGKTLATVD 378 Query: 329 TTSIVPVDLNSLMFKMEKILARASKAAGDNAMANQYETLANARQKGIEKYLWNDQQGWYA 388 TS+ P+DLN L+ +E+ LA+A + GD A A R I + LW+ Q + Sbjct: 379 VTSLAPIDLNCLIVDLERALAKAYRVRGDVTHAENMSQRAATRADTIRRVLWDPQLQAFG 438 Query: 389 DYDLKSHKVRNQLTAAALFPLYVNAAAKDRANKMATATKTHLLQPGGLNTTSVKSGQQWD 448 DYD + ++LTAA ++PLY A++ +A +A + LL+PGGL TT V +GQQWD Sbjct: 439 DYDFVHRTLTHRLTAATVYPLYTGVASRQQAKAVAATLQRELLRPGGLATTRVATGQQWD 498 Query: 449 APNGWAPLQWVATEGLQNYGQKEVAMDISWHFL-TNVQHTYDREKKLVEKYDV--STTGT 505 APNGWAPLQ++A GL+ Y + +A I+ ++ TNV + Y KLVEKYDV ++ G Sbjct: 499 APNGWAPLQYLAVIGLRRYSEPALAQTIATRWIKTNVSY-YQHTGKLVEKYDVDAASPGV 557 Query: 506 GGGGGEYPLQDGFGWTNGVTLKMLDLI-------CPKEQPCDNVPATRPTVKSATTQPST 558 GGGEYPLQDGFGWTNGV +L L P + P + +A +T Sbjct: 558 SAGGGEYPLQDGFGWTNGVLRTLLALYPQAAGTSRPSDIPAGPAGVSAAAASAAAASKNT 617 Query: 559 KEAQPT 564 Q T Sbjct: 618 HRLQGT 623 Lambda K H 0.315 0.132 0.409 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: 1050 Number of extensions: 39 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: 565 Length of database: 627 Length adjustment: 37 Effective length of query: 528 Effective length of database: 590 Effective search space: 311520 Effective search space used: 311520 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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