Align alpha,alpha-trehalase (EC 3.2.1.28) (characterized)
to candidate RR42_RS28230 RR42_RS28230 trehalase
Query= BRENDA::D4I261 (536 letters) >FitnessBrowser__Cup4G11:RR42_RS28230 Length = 536 Score = 578 bits (1491), Expect = e-169 Identities = 287/510 (56%), Positives = 359/510 (70%), Gaps = 4/510 (0%) Query: 28 PEPIRGLPASDTLTPSDRYQDLFAAVQLSHIFSDSKTFADCAPKTDPQHILFRYYLERER 87 P + G +D LTP+DRYQ+LF AVQ+ IF DSKTF D P+ DP IL Y Sbjct: 12 PHRLAGCAHADPLTPADRYQELFVAVQMGRIFPDSKTFTDAMPRQDPATILAAYRARAGA 71 Query: 88 EEFNLLEFVLENFDLPSVHESRYVSDPDNTMTEHIDGLWPVLTRQPEKHRKFSSLLPLPR 147 F+L FV +F LP V S Y SDP+ + +HIDGLW VLTR P +H SLLPLP Sbjct: 72 AGFDLAAFVHAHFALPEVPRSCYESDPNQPLADHIDGLWAVLTRHPAQHPPQCSLLPLPH 131 Query: 148 PYVVPGGRFSEAYYWDSYFSMLGFAAAGRGELMRSMADNFAWMIDKYGHIPNGNRTYYLS 207 PYVVPGGRFSE YYWDSYF+MLG AA+G+G L+R MA+NF++++D YG IPNG R+YYLS Sbjct: 132 PYVVPGGRFSELYYWDSYFTMLGLAASGQGGLLRGMAENFSYLLDTYGVIPNGTRSYYLS 191 Query: 208 RSQPPVFAMMVELFEKNNVHEAQHYLPQLKSEYEFWMDGQATLSSNQAYRHVVMLDDGSV 267 RSQPPVFA+MVELFE V +LPQL+ EY FWM G L+ QA R VV L DGS+ Sbjct: 192 RSQPPVFALMVELFEDQGVQPELGFLPQLRKEYAFWMRGADCLAPGQACRRVVRLADGSL 251 Query: 268 LNRYWDDRDTPRDESYREDVETARHSSRPSSEVYRDLRAGAASGWDYTSRWLSEPGHLES 327 LNRYWD+RDTPR+E++ ED TA ++RP++EV+RDLRA A SGWD++SRW G LE+ Sbjct: 252 LNRYWDERDTPREEAFIEDTGTAALAARPAAEVFRDLRAAAESGWDFSSRWQEPGGGLET 311 Query: 328 IQTTSIVPIDLNAFLYKLETTIARLSASKGDLDAADRFQQLALRRREAVDKFLWDEPAGL 387 ++TT+I+P+DLN L+KLE +A L+ + GD D A F Q A RREA+D+ +W E G Sbjct: 312 VRTTAILPVDLNCLLFKLEHKLAELAQAAGDAD-APVFAQRAQARREAIDRLMWREAEGA 370 Query: 388 YRDYNW-REGEQATFSAAAVTPLYVGMASLDQASRTAKAVRDHLLAPGGILCSMNVTGEQ 446 Y D++W R +A +AA V PLYVG A+ QA+R A+ V LL PGGI + V+G+Q Sbjct: 371 YFDFDWQRHHARANLTAATVVPLYVGAATPAQAARVAQTVAARLLQPGGIATTERVSGQQ 430 Query: 447 WDSPNGWAPVQWMAIKGFHSYGNELLAQEIASRWLHTVSSTWQQHHKMVEKYNI--SGDA 504 WD PNGWAP+QW+AI GF G LA EIA RWL TV+S +Q+ +K+VEKY + D Sbjct: 431 WDLPNGWAPLQWLAIGGFACCGQAALAHEIAHRWLVTVASLYQREYKLVEKYALQPGEDG 490 Query: 505 ALLGGGGEYPLQDGFGWTNGVTRRLLEMYP 534 A+ GGGGEYPLQDGFGWTNGV RRLL+ +P Sbjct: 491 AVGGGGGEYPLQDGFGWTNGVVRRLLQDHP 520 Lambda K H 0.318 0.134 0.421 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: 905 Number of extensions: 36 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: 536 Length of database: 536 Length adjustment: 35 Effective length of query: 501 Effective length of database: 501 Effective search space: 251001 Effective search space used: 251001 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 (21.7 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