Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 14407 b0269 CP4-6 prophage; predicted dehydratase (NCBI)
Query= reanno::Smeli:SM_b20890 (579 letters) >FitnessBrowser__Keio:14407 Length = 655 Score = 192 bits (487), Expect = 5e-53 Identities = 148/453 (32%), Positives = 230/453 (50%), Gaps = 39/453 (8%) Query: 98 AMMFRNLAAMDVEESIRGNPVDGVVL-LGGCDKTTPSLLMGAASV-DIPAIVVSGGPMLN 155 ++ +RN AA+ IR P V+ + CDK P+ ++ A++ D+P I+V GG L Sbjct: 132 SLPYRNDAAIVFRRLIRSLPTRRAVIGVATCDKGLPATMIALAAMHDLPTILVPGGATLP 191 Query: 156 GKWRGKDVGSGTAIWQFSEMVKSGEMSLEEFMDAE-QGMARSAGSCMTMGTASTMASMAE 214 G+D G I + E+SL+E + + A G C +GTA T +AE Sbjct: 192 PTV-GEDAGKVQTI---GARFANHELSLQEAAELGCRACASPGGGCQFLGTAGTSQVVAE 247 Query: 215 ALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVKEDLKPSDILTKEAFENAIRVNGAVG 274 ALG+ L +A P+ A I++ + R + E+ + DIL+ +A ENA+ ++ A G Sbjct: 248 ALGLALPHSALAPSGQAVWLEIARQSARAVSELDSRGITTRDILSDKAIENAMVIHAAFG 307 Query: 275 GSTNAVLHLLALAGRVGVDL-SLDDWDRLGRDVPTIVNLQPSGK--YLMEEFYYAGGLPV 331 GSTN +LH+ A+A G + ++ W R+ R VP +V++ P+G + + AGG+P Sbjct: 308 GSTNLLLHIPAIAHAAGCTIPDVEHWTRINRKVPRLVSVLPNGPDYHPTVRAFLAGGVPE 367 Query: 332 VIKAVAEMGLLHNDAITVSGDTI------WNDVKGVVNYN-----------EDVILPREK 374 V+ + ++GLLH DA+TV+G T+ W + + +DVILP EK Sbjct: 368 VMLHLRDLGLLHLDAMTVTGQTVGENLEWWQASERRARFRQCLREQDGVEPDDVILPPEK 427 Query: 375 ALTK--SGGIAVLRGNLAPRGAVLKPSAASPHLM------QHKGRAVVFESIEDYHARIN 426 A K + + GN+AP G+V+K +A P ++ H GR VF S I Sbjct: 428 AKAKGLTSTVCFPTGNIAPEGSVIKATAIDPSVVGEDGVYHHTGRVRVFVSEAQAIKAIK 487 Query: 427 REDLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMIRISDARMSGTAYGT 486 RE +I + IMV+ GP G GM E + K + G T + I+DAR SG + G Sbjct: 488 RE--EIVQGDIMVVIGGGPSG-TGMEETYQLTSALKHISWGKTVSL-ITDARFSGVSTGA 543 Query: 487 VILHTAPEAAEGGPLALVENGDLIEVDIPNRTL 519 H +PEA GGP+ + + D+IE+ + TL Sbjct: 544 CFGHVSPEALAGGPIGKLRDNDIIEIAVDRLTL 576 Lambda K H 0.318 0.135 0.402 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: 1018 Number of extensions: 69 Number of successful extensions: 7 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: 579 Length of database: 655 Length adjustment: 37 Effective length of query: 542 Effective length of database: 618 Effective search space: 334956 Effective search space used: 334956 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: 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