Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate BWI76_RS24725 BWI76_RS24725 altronate hydrolase
Query= reanno::WCS417:GFF829 (517 letters) >FitnessBrowser__Koxy:BWI76_RS24725 Length = 495 Score = 233 bits (595), Expect = 9e-66 Identities = 167/492 (33%), Positives = 241/492 (48%), Gaps = 16/492 (3%) Query: 13 IRLHERDNVVIVVNDQGVPAGTEFPDGLVTV-DFIPQSHKVTLEDIPEGGQIIRYGQTIG 71 I++H DNV + + D VT+ I + HK TL I +G +I+YG IG Sbjct: 4 IKIHSHDNVAVALADMAAGTVVTIDGDTVTLAQDIARGHKFTLRGIAKGDNVIKYGLPIG 63 Query: 72 YALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGYRNADGTVGTRN 131 +ALA I G + R + LD+ ++ E A + YR A+G VG RN Sbjct: 64 HALADIAPGEHIHSHNTRTNLSD-LDAYSYQPDLSEPAAQPADRDIQIYRRANGEVGVRN 122 Query: 132 ILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAITATDAYIPIRT 191 L I TV CV + R E +D V +H+YGC D +I RT Sbjct: 123 ELWILPTVGCVNAMARQMQNRFLKETNDA-EGIDGVHLFSHTYGCS---QLGDDHINTRT 178 Query: 192 V-RNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQDSSHGFTEMIE 250 + +N+ R+PN G LV+ LGCE Q + D Q +E Sbjct: 179 MLQNMVRHPNAGA-VLVVGLGCENNQV-DAFRETLGEFDPERVHFMICQHQDDEVEAGLE 236 Query: 251 QIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYASDLLLRAGAT 310 + L + + +RE+ SEL G++CGGSD SGITANP LG SD L+ G T Sbjct: 237 HLRQLYDV----MRHDKRESGKLSELKFGLECGGSDGLSGITANPMLGRFSDYLIANGGT 292 Query: 311 VMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSANTTPGNKKGGL 370 + +EV E+ A LL S + + +LV ++ + +Y + N +PGNK GG+ Sbjct: 293 TVLTEVPEMFGAEQLLMSHCRDEETFGKLVTMVNDFKQYFLAHDQPIYENPSPGNKAGGI 352 Query: 371 SNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQLAAGMNLHVF 430 + + +KSLG K+GSS + VL GER K GL + P +D V + AG ++ +F Sbjct: 353 TTLEDKSLGCTQKAGSSQVVDVLRYGERLKVHGLNLLSAPGNDAVATSALAGAGCHMVLF 412 Query: 431 TTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELGWELFHFYLDV 490 +TGRGTPYG P VK++T +ELA + ID DAG++ G+A + +L E +D Sbjct: 413 STGRGTPYG-GFVPTVKIATNSELATKKKHWIDFDAGQLIHGKA-MPQLLEEFVDTIVDF 470 Query: 491 ASGRKQTWAEHH 502 A+G KQT E + Sbjct: 471 ANG-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: 642 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