Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate 17166 b3091 altronate hydrolase (NCBI)
Query= reanno::WCS417:GFF829 (517 letters) >FitnessBrowser__Keio:17166 Length = 495 Score = 234 bits (596), Expect = 7e-66 Identities = 170/494 (34%), Positives = 240/494 (48%), Gaps = 20/494 (4%) Query: 13 IRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDF---IPQSHKVTLEDIPEGGQIIRYGQT 69 I++H DNV + + D + GTE TV + + HK L DI +G +I+YG Sbjct: 4 IKIHALDNVAVALAD--LAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLP 61 Query: 70 IGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGYRNADGTVGT 129 IGYALA I G V R + LD + + A + YR A+G VG Sbjct: 62 IGYALADIAAGVHVHAHNTRTNLSD-LDQYRYQPDFQDLPAQAADREVQIYRRANGDVGV 120 Query: 130 RNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAITATDAYIPI 189 RN L I TV CV G+ R E D V +H+YGC D +I Sbjct: 121 RNELWILPTVGCVNGIARQIQNRFLKET-NNAEGTDGVFLFSHTYGCS---QLGDDHINT 176 Query: 190 RTV-RNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQDSSHGFTEM 248 RT+ +N+ R+PN G LVI LGCE Q + +D Q Sbjct: 177 RTMLQNMVRHPNAGA-VLVIGLGCENNQVA-AFRETLGDIDPERVHFMICQQQDDEIEAG 234 Query: 249 IEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYASDLLLRAG 308 IE + L + +RE SEL G++CGGSD SGITANP LG SD ++ G Sbjct: 235 IEHLHQLYNV----MRNDKREPGKLSELKFGLECGGSDGLSGITANPMLGRFSDYVIANG 290 Query: 309 ATVMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSANTTPGNKKG 368 T + +EV E+ A LL + ++LV ++ + +Y + N +PGNK G Sbjct: 291 GTTVLTEVPEMFGAEQLLMDHCRDEATFEKLVTMVNDFKQYFIAHDQPIYENPSPGNKAG 350 Query: 369 GLSNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQLAAGMNLH 428 G++ + +KSLG K+GSS + VL GER K GL + P +D V + AG ++ Sbjct: 351 GITTLEDKSLGCTQKAGSSVVVDVLRYGERLKTPGLNLLSAPGNDAVATSALAGAGCHMV 410 Query: 429 VFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELGWELFHFYL 488 +F+TGRGTPYG P VK++T +ELA + ID DAG++ G+A + +L E + Sbjct: 411 LFSTGRGTPYG-GFVPTVKIATNSELAAKKKHWIDFDAGQLIHGKA-MPQLLEEFIDTIV 468 Query: 489 DVASGRKQTWAEHH 502 + A+G KQT E + Sbjct: 469 EFANG-KQTCNERN 481 Lambda K H 0.318 0.135 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: 636 Number of extensions: 33 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: 517 Length of database: 495 Length adjustment: 34 Effective length of query: 483 Effective length of database: 461 Effective search space: 222663 Effective search space used: 222663 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