Align trehalose-6-phosphate hydrolase (TreC;KP1_0530) (EC 3.2.1.93) (characterized)
to candidate AZOBR_RS25735 AZOBR_RS25735 alpha-amylase
Query= CAZy::BAG86620.1 (551 letters) >FitnessBrowser__azobra:AZOBR_RS25735 Length = 537 Score = 363 bits (932), Expect = e-105 Identities = 215/559 (38%), Positives = 299/559 (53%), Gaps = 59/559 (10%) Query: 7 WWQNGVIYQIYPKSFQDTTGSGTGDLRGVTARLDYLQKLGVDAIWLTPFYVSPQVDNGYD 66 WWQ+GVIYQ+YP+SFQD+ G G GDL G+ ARLD+LQ LGVDA+W++P Y SP D GYD Sbjct: 7 WWQSGVIYQVYPRSFQDSNGDGVGDLPGILARLDHLQTLGVDALWVSPIYPSPMADFGYD 66 Query: 67 VANYTAIDPSYGTMADFDALVAEAKARGIRIVLDMVLNHTSTEHEWFRQS-LNKESPYRQ 125 V++YT + P +GTM DF+ L+AE RG++++LD V NH+S H WF+ S +++ P R Sbjct: 67 VSDYTGVHPLFGTMEDFERLLAELHRRGMKLILDFVPNHSSDRHPWFQASRSSRDDPKRD 126 Query: 126 FYIWRDGEPD-ALPNNWRSKFGGNAWQWHADSGQYYLHLFAIEQADLNWENPAVRAELKK 184 +YIWRD PD PNNW S+FGG AW+W A +GQYY H + EQ DLNW NPA+R + Sbjct: 127 WYIWRDAAPDGGPPNNWLSEFGGGAWEWDAATGQYYYHAYLKEQPDLNWRNPALREAMLD 186 Query: 185 VCEFWADRGVDGLRLDVVNLISKDQTFPCDLDGDG------------RRFYTDGPRVHEF 232 W DRGVDG R+D ++ + KD F + G R D P VH+ Sbjct: 187 ALRVWLDRGVDGFRVDAIHHLIKDAQFRDNPPNPGWREGMSPVRRLIRLHTVDQPEVHDA 246 Query: 233 LQEMSR--DVFTPRNLMTVGEMSSTSLEHCQQYAALDGRELSMTFNFHHLKVDYPGGEKW 290 + M R D + P L+ +GE + ++ Y D + FNFH L + Sbjct: 247 IAAMRRVADGYGPDRLL-IGE-AYLPIDQLMAYYGADLTGFQLPFNFHLLSTPW------ 298 Query: 291 TLARPDYVALKALFRHWQQGMHNRAWNALFWCNHDQPRIVSRFGDEGEYRVTAAKMLAMV 350 + AL AL R ++ + W NHD+ R+ SR G G+ RV AM+ Sbjct: 299 -----EAKALAALIRTYEAALPPGGWPNWVLGNHDRSRVASRLG-RGQARVA-----AML 347 Query: 351 LHGMQGTPYIYQGEEIGMTNPHFSSISDYRDVESHNMFIERAAQGQSPDELLAILASKSR 410 L ++GTP +YQG+EIGMT+ + Q P E R Sbjct: 348 LLTLRGTPTLYQGDEIGMTDVAIP-----------------PDRVQDPWEKNIPGLGLGR 390 Query: 411 DNSRTPMPWHAGENGGFSDGEPWIGLGDNYQEINVEAALADPDSVFYTYQQLITLRKTLP 470 D RTP+PW G GGF+ GEPW+ LG +++ +NV A ADP S+ ++ L++LR+ P Sbjct: 391 DPVRTPIPWDGGPRGGFTTGEPWLPLGPDHERVNVAAQAADPSSMLALHRALLSLRRAEP 450 Query: 471 LLTWGDYEDLLPEHPSLWCYRRQWQGQTLVVAANLSRELQAWQPAEA-PGEWKMIISNYA 529 L+ G YE + E+ L Y R+ V NLS A + +A P + +S + Sbjct: 451 ALSVGRYEPVSAENDVL-VYERRHGRDRFRVLLNLS---AAERTVDAVPDAAHIRLSTHL 506 Query: 530 ETTPRPT--GLTLRPFEAI 546 + P L LRP E + Sbjct: 507 DRGGEPVSGALRLRPDEGV 525 Lambda K H 0.320 0.136 0.446 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: 1022 Number of extensions: 54 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: 551 Length of database: 537 Length adjustment: 35 Effective length of query: 516 Effective length of database: 502 Effective search space: 259032 Effective search space used: 259032 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 (21.8 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