Align alpha,alpha-trehalase (EC 3.2.1.28) (characterized)
to candidate Ga0059261_0579 Ga0059261_0579 Neutral trehalase
Query= BRENDA::P13482 (565 letters) >FitnessBrowser__Korea:Ga0059261_0579 Length = 495 Score = 491 bits (1263), Expect = e-143 Identities = 255/493 (51%), Positives = 319/493 (64%), Gaps = 5/493 (1%) Query: 37 PQPPDILLGPLFNDVQNAKLFPDQKTFADAVPNSDPLMILADYRMQQNQSGFDLRHFVNV 96 PQP D L G LF VQ LFPD KTFADAVP P I+ D++ Q LR FV+ Sbjct: 4 PQPSD-LFGDLFTTVQECALFPDSKTFADAVPRRGPEAIMQDWKAQPPSGDAGLRAFVDA 62 Query: 97 NFTLPKEGEKYVPPEGQSLREHIDGLWPVLTRSTENTEKWDSLLPLPEPYVVPGGRFREV 156 NF LP E + P +G+ LREHI LWPVLTR E SLL LP +VVPGGRFRE+ Sbjct: 63 NFVLPTEADCDAP-DGRPLREHITQLWPVLTREPETPAPGSSLLALPRRHVVPGGRFREL 121 Query: 157 YYWDSYFTMLGLAESGHWDKVADMVANFAHEIDTYGHIPNGNRSYYLSRSQPPFFALMVE 216 YYWDSYFTMLGL S D V DM+A F +D YGHIPNG RSYYLSRS PP F LM Sbjct: 122 YYWDSYFTMLGLVRSDRQDLVEDMIAVFGSLLDGYGHIPNGTRSYYLSRSHPPVFYLMAA 181 Query: 217 LLAQHEGDAALKQYLPQMQKEYAYWMDGVENLQAGQQEKRVVKLQDGTLLNRYWDDRDTP 276 L +Q A Q L M+ E+ +WM G ++L G + +RVV+L DG LLNRYWDDR P Sbjct: 182 L-SQDRSANARAQRLSWMRAEHEFWMAGEKDLAPGGEHRRVVRLADGALLNRYWDDRAAP 240 Query: 277 RPESWVEDIATAKSNPNRPATEIYRDLRSAAASGWDFSSRWMDNPQQLNTLRTTSIVPVD 336 R ESW EDI A+ P+R A E++RD+R+AA SGWDFSSRW+ + Q L T+RTT ++P+D Sbjct: 241 RDESWREDIELAQRAPDRDAPELWRDIRAAAESGWDFSSRWLGDGQSLETIRTTRLLPID 300 Query: 337 LNSLMFKMEKILARASKAAGDNAMANQYETLANARQKGIEKYLWNDQQGWYADYDLKSHK 396 LN+L+F +E+ +A +KA GD+ A ++ A+AR++ I+ +LW+ +YADYDL + Sbjct: 301 LNALLFGLEQAIAEEAKALGDDTAATEFARRADARREAIDLHLWHPDAAFYADYDLDLGR 360 Query: 397 VRNQLTAAALFPLYVNAAAKDRANKMATATKTHLLQPGGLNTTSVKSGQQWDAPNGWAPL 456 +LTAA F L+ A+ RA A A LL+ GGL TT +GQQWDAPNGWAPL Sbjct: 361 ASGRLTAALGFALFTGVASAQRAPDAANAI-AGLLRAGGLLTTECVTGQQWDAPNGWAPL 419 Query: 457 QWVATEGLQNYGQKEVAMDISWHFLTNVQHTYDREKKLVEKYDVSTTGTGGGGGEYPLQD 516 WV EGL+ YGQ +A I+ +L V YD +L+EKYD+ GGGGEY + Sbjct: 420 HWVVIEGLRAYGQNALADTIAQRWLAMVASHYDATGQLLEKYDIEQC-RAGGGGEYGTEI 478 Query: 517 GFGWTNGVTLKML 529 GFGWTNGVTL ++ Sbjct: 479 GFGWTNGVTLALM 491 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: 874 Number of extensions: 42 Number of successful extensions: 5 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: 495 Length adjustment: 35 Effective length of query: 530 Effective length of database: 460 Effective search space: 243800 Effective search space used: 243800 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: 52 (24.6 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