Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate Ga0059261_2974 Ga0059261_2974 Altronate dehydratase
Query= reanno::WCS417:GFF829 (517 letters) >FitnessBrowser__Korea:Ga0059261_2974 Length = 490 Score = 211 bits (536), Expect = 6e-59 Identities = 150/463 (32%), Positives = 226/463 (48%), Gaps = 16/463 (3%) Query: 9 SPRSIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFIPQSHKVTLEDIPEGGQIIRYGQ 68 +P ++R+H D V + + + AG E G+ D IP++HK L G ++++G Sbjct: 2 NPAALRIHGADTVATALRN--LVAG-EVVLGVTLSDAIPRAHKFALVAHAPGDPVLKFGF 58 Query: 69 TIGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGYRNADGTVG 128 IG A A I G V + A + A A + GY ADG G Sbjct: 59 PIGRATAAIAPGDHVHVHNVATALAGEA-AYGGGAGAERAPAAASAIKWRGYPRADGRAG 117 Query: 129 TRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAITATDAYIP 188 TRN + I TV CV G + + LLP VD V A H +GC D Sbjct: 118 TRNEIWILPTVGCV-GRTAQKIAVKAEALLPA--GVDGVHAFAHPFGCSQLSDDLDGTRN 174 Query: 189 IRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQDSSHGFTEM 248 I + LA++PN GG L++ LGCE Q ++ V + + Q S E Sbjct: 175 ILSA--LAQHPNAGG-VLLVGLGCESNQLSALLETLPEDVRMRVRTV-GAQSSPDEIGEG 230 Query: 249 IEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYASDLLLRAG 308 + +++ LA+ +RE + L+LG++CGGSD SG+TANP +G +D + AG Sbjct: 231 VGKVLELAQLAATA----QREEMGLDRLVLGVKCGGSDGLSGLTANPLVGIMADRITDAG 286 Query: 309 ATVMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSANTTPGNKKG 368 + + +E+ E+ A LL +RA + + ++ + RY S N +PGN G Sbjct: 287 GSAILTEIPEIFGAEQLLMARAADADTFDAIGALVNRFKRYFIDHGEPVSENPSPGNIAG 346 Query: 369 GLSNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQLAAGMNLH 428 G++ + EKSLG++ K G + + V+ G+R K GL P +D V T AAG + Sbjct: 347 GITTLEEKSLGAVQKGGQAIVTDVIDYGDRVKRTGLTLLEAPGNDAVSSTALSAAGATVI 406 Query: 429 VFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIAT 471 +FTTGRGTP G AP +K+++ ++LA R P ID DAG++ T Sbjct: 407 LFTTGRGTPLGFP-APTLKIASNSDLAARKPGWIDFDAGQVLT 448 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: 661 Number of extensions: 23 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: 517 Length of database: 490 Length adjustment: 34 Effective length of query: 483 Effective length of database: 456 Effective search space: 220248 Effective search space used: 220248 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 Apr 09 2024. 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