Align Probable galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (uncharacterized)
to candidate H281DRAFT_00666 H281DRAFT_00666 altronate hydrolase
Query= curated2:P42240 (510 letters) >FitnessBrowser__Burk376:H281DRAFT_00666 Length = 518 Score = 312 bits (800), Expect = 2e-89 Identities = 194/499 (38%), Positives = 269/499 (53%), Gaps = 20/499 (4%) Query: 3 MNLRKNQA----PLYIKVHEIDNTAIIVNDGGLPKGT-VFSCGLVLEEDVPQGHKVALTD 57 MN+ +Q+ P I++H D+ I L G + S LV+ +P GHK+A Sbjct: 1 MNIMSSQSTQSDPAVIRLHANDDVVIATRQ--LMSGARIASEDLVIAGLIPPGHKIATRA 58 Query: 58 LNQGDEIVRYGEVIGFADETIKRGSWIREALVRMPAPPALDDLPLANRVPQPRPPLEGYT 117 + G+ + RY ++IG A + I+RG + + M + +A Q E T Sbjct: 59 IAAGEPVKRYNQIIGVATQPIQRGQHVHVQNLGMAEFSRAHEFGVAVHATQYAA--EPAT 116 Query: 118 FEGYRNADGSAGTKNILGITTSVQCVV----GVLDYAVKRIKEELLPKYPNVDDVVPLHH 173 F G R ADG T+N +G+ TSV C + D+ + + L YPNVD VV L H Sbjct: 117 FMGIRRADGRVATRNYIGVLTSVNCSATVARAIADHFRRDVNPHALADYPNVDGVVALTH 176 Query: 174 QYGCGVAINAPDAVIPIRTIQNLAKHPNFGGEVMVIGLGCEKL----LPERIASENDDDI 229 GCG+ + RT+ A HPNF V+ +GLGCE + E ++ + + Sbjct: 177 GLGCGIDTLGEGLAVLRRTLAGYAVHPNFHS-VLFVGLGCETNQIAGVLESAGLKDTEQL 235 Query: 230 LS--LQDHRGFAAMIQSILEMAEERLIRLNSRTRVSCPVSDLVIGLQCGGSDAFSGVTAN 287 S +QD G I+ + M E L N R P S L++GLQCGGSD +SG++AN Sbjct: 236 RSFTIQDSGGSKKTIERGIAMVNEMLADANRVKREPLPASHLIVGLQCGGSDGYSGISAN 295 Query: 288 PAVGYAADLLVRAGATVLFSEVTEVRDAIHLLTPRAVSEEVGQSLIKEMKWYDSYLRRGD 347 PA+G A DLLV+ G T + SE EV A HLLT RAVS VG+ L+ + W++ Y R Sbjct: 296 PALGAAVDLLVQHGGTAILSETPEVYGAEHLLTRRAVSRAVGEKLLARIAWWEEYCARNG 355 Query: 348 ADRSANPSPGNKKGGLSNVVEKALGSVAKSGTSPISGVLGPGERAKQKGLLFAATPASDF 407 A NPS GNK GGL+ ++EK+LG+VAK GT+ + V ER KG +F +P D Sbjct: 356 AALDNNPSAGNKVGGLTTILEKSLGAVAKGGTTNLVDVYQYAERIDAKGFVFMDSPGYDP 415 Query: 408 VCGTLQLAAGMNLQVFTTGRGTPYGLAAAPVLKVSTRHSLSEHWADLIDINAGRIATGEA 467 V T Q+AAG NL FTTGRG+ YG A +P LK++T +L E D +DIN G + G A Sbjct: 416 VSATGQVAAGANLICFTTGRGSAYGCAPSPSLKLATNTALWERQEDDMDINCGGVIDGSA 475 Query: 468 SIEDVGWEIFRTILDVASG 486 SIE++G IF +L+ ASG Sbjct: 476 SIEELGEAIFAQMLECASG 494 Lambda K H 0.318 0.136 0.406 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: 684 Number of extensions: 39 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: 510 Length of database: 518 Length adjustment: 35 Effective length of query: 475 Effective length of database: 483 Effective search space: 229425 Effective search space used: 229425 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