Align alpha,alpha-trehalase (EC 3.2.1.28) (characterized)
to candidate BWI76_RS17700 BWI76_RS17700 alpha,alpha-trehalase
Query= BRENDA::A4WBE4 (568 letters) >FitnessBrowser__Koxy:BWI76_RS17700 Length = 582 Score = 930 bits (2404), Expect = 0.0 Identities = 441/563 (78%), Positives = 496/563 (88%), Gaps = 4/563 (0%) Query: 7 RRPAALPLALRVALGGALLGVAAFSHAEEAQSTQKQSPDILLGPLFVDVQSAKLFPDQKT 66 RRPA LP ALR+ALGGA + +A + E QSPDILLGPLF DVQSAKLF DQKT Sbjct: 7 RRPATLPYALRLALGGAFVALATLTAQAEETRPIPQSPDILLGPLFNDVQSAKLFSDQKT 66 Query: 67 FADAVPKSDPLMILADYRMQHKQSGFDLRHFVEMNFTLPGEGEKYVPPAGQNLREHIDGL 126 FADA+P DPLMILADYRMQ Q+ FDLRHFVE+NFTLP E ++YVPP GQ LR+HI+GL Sbjct: 67 FADAIPNGDPLMILADYRMQKSQTSFDLRHFVELNFTLPRENDQYVPPKGQTLRQHINGL 126 Query: 127 WPVLTRTTDKASKWDSLLPLPKPYVVPGGRFREVYYWDSYFTMLGLAESGHWDKISDMVA 186 WPVLTR+T + KWDSLLPLPKPYVVPGGRFREVYYWDSYFTMLGLAESGHWDKI DMV Sbjct: 127 WPVLTRSTVEVEKWDSLLPLPKPYVVPGGRFREVYYWDSYFTMLGLAESGHWDKIEDMVT 186 Query: 187 NFGYELDSWGHIPNGNRSYYLSRSQPPFFSLMVELLATHD-KEALKTYRAQMEKEYAYWM 245 NF E+D+WGHIPNGNR+YYLSRSQPPFF MVELLATHD EALK + QMEKEY YWM Sbjct: 187 NFAAEIDAWGHIPNGNRTYYLSRSQPPFFPFMVELLATHDGDEALKKWLPQMEKEYQYWM 246 Query: 246 EGAETLQPGQANKRVVKLDDGSILNRYWDDRDTPRPESWLDDVTTAKNNPNRPATEIYRD 305 +GAE L+PG A+KRVV++ DGS+LNRYWDD DTPRPESWLDDVTTAKNNPNRPATEIYRD Sbjct: 247 DGAEALEPGGASKRVVRMADGSLLNRYWDDNDTPRPESWLDDVTTAKNNPNRPATEIYRD 306 Query: 306 LRSAAASGWDFSSRWMDDPQKLGTIRTTSIVPVDLNALMFKMEKLLAKASQESGDAAATS 365 LRSAAASGWDFSSRWMD+PQ+LGTIRTTSIVPVDLN+LMF MEK +A+AS+ +GD+A + Sbjct: 307 LRSAAASGWDFSSRWMDNPQQLGTIRTTSIVPVDLNSLMFHMEKAIARASKAAGDSAKAA 366 Query: 366 KYETLATSRQKAMESHLWNEKEGWYADYDLKSKKVRNQLTAAALFPLYVNAASNDRAAKV 425 +Y+ LA +RQKA+E +LWN+KEGWYADYDLKS KVRNQLTAAALFPLYVNAAS++RAAKV Sbjct: 367 QYDALANARQKALEKYLWNDKEGWYADYDLKSHKVRNQLTAAALFPLYVNAASSERAAKV 426 Query: 426 ASATASRLLKPGGISTTTINSGQQWDAPNGWAPLQWVATEGLQNYGHEKVAMDVTWRFLT 485 A+AT +RLLKPGG++TTT+NSGQQWDAPNGWAPLQWVA EGLQ YG +K+AM+V+WRFL+ Sbjct: 427 AAATEARLLKPGGLTTTTVNSGQQWDAPNGWAPLQWVAAEGLQKYGQQKIAMEVSWRFLS 486 Query: 486 NVQHTYDREQKLVEKYDVSTTGTGGGGGEYPLQDGFGWTNGVTLKMLDLVCPKEKPCDSV 545 NVQHTY+ EQKLVEKYDVS+TGTGGGGGEYPLQDGFGWTNGVTLKMLDLVCPKEKPCDSV Sbjct: 487 NVQHTYNSEQKLVEKYDVSSTGTGGGGGEYPLQDGFGWTNGVTLKMLDLVCPKEKPCDSV 546 Query: 546 PASQPAANDDVAPQSSTEKSAAQ 568 PA++PAANDD S +AAQ Sbjct: 547 PATRPAANDDT---SKATDNAAQ 566 Lambda K H 0.315 0.131 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: 1181 Number of extensions: 38 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 568 Length of database: 582 Length adjustment: 36 Effective length of query: 532 Effective length of database: 546 Effective search space: 290472 Effective search space used: 290472 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