Align Probable galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (uncharacterized)
to candidate CCNA_01555 CCNA_01555 altronate dehydratase
Query= curated2:P42240 (510 letters) >FitnessBrowser__Caulo:CCNA_01555 Length = 502 Score = 238 bits (606), Expect = 5e-67 Identities = 155/454 (34%), Positives = 237/454 (52%), Gaps = 22/454 (4%) Query: 42 VLEEDVPQGHKVALTDLNQGDEIVRYGEVIGFADETIKRGSWIR--EALVRMPAPPALDD 99 ++ DVP+GHK+A + GD++++YG IG A I G + + R+ Sbjct: 42 IVRADVPKGHKIATRVVRSGDDVLKYGWPIGRATADIAVGDHVHVHNVITRLEGVEGYAF 101 Query: 100 LPLANRVPQPRPPLEGYTFEGYRNADGSAGTKNILGITTSVQCVVGVLDYAVKRIKEELL 159 PL P P + TF+G+R +G AGT+N + + +V CV +RI E+ Sbjct: 102 APLP---PAGAPSADTRTFQGFRRKNGRAGTRNEIWVLCTVGCVANT----ARRIAEKAN 154 Query: 160 PKYPN-VDDVVPLHHQYGCGVAINAPDAVIPIRTIQNLAKHPNFGGEVMVIGLGCEKLLP 218 ++ VD V H +GC D + I LA HPN GG V+++GLGCE Sbjct: 155 QRFAGRVDGVYAFPHPFGCSQL--GDDLAHTRKLIAALASHPNAGG-VLILGLGCENNQL 211 Query: 219 ERIASENDDDILSLQDHRGFAA-MIQSILE---MAEERLIRLNSRTRVS-CPVSDLVIGL 273 + + D + + +GF M++ LE A E L+ + + R PVS+LV+GL Sbjct: 212 KALLESAPD--IDRERLKGFTTQMVEDELEDGLAAVEALVEIAEKDRREPVPVSELVVGL 269 Query: 274 QCGGSDAFSGVTANPAVGYAADLLVRAGATVLFSEVTEVRDAIHLLTPRAVSEEVGQSLI 333 +CGGSD FSG+TANP VG AD + AG T + +E+ E+ A ++L RA S EV + + Sbjct: 270 KCGGSDGFSGITANPLVGRIADKVAEAGGTPVLTEIPEIFGAENVLLQRAASREVFDAAV 329 Query: 334 KEMKWYDSYLRRGDADRSANPSPGNKKGGLSNVVEKALGSVAKSGTSPISGVLGPGERAK 393 + + Y + NPSPGN GG++++ EK+LG+V K G +P+ VL GE Sbjct: 330 AVIDDFKRYFIEANQPIYENPSPGNIAGGITSLEEKSLGAVQKGGRAPLVEVLRYGETVG 389 Query: 394 QKGLLFAATPASDFVCGTLQLAAGMNLQVFTTGRGTPYGLAAAPVLKVSTRHSLSEHWAD 453 + GL P +D V T AAG + +FTTGRGTP G AP LK+++ L++ Sbjct: 390 RHGLTLLEAPGNDAVSSTALTAAGATVILFTTGRGTPLGF-PAPTLKIASNSGLAQRKPG 448 Query: 454 LIDINAGRIATGEASIEDVGWEIFRTILDVASGR 487 ID +AG++ G S++ + +++ ASG+ Sbjct: 449 WIDFDAGQVLEG-VSMDVAAENLMDLVIETASGK 481 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: 660 Number of extensions: 42 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: 510 Length of database: 502 Length adjustment: 34 Effective length of query: 476 Effective length of database: 468 Effective search space: 222768 Effective search space used: 222768 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