Align phosphogluconate dehydratase (characterized)
to candidate CCNA_00862 CCNA_00862 xylonate dehydratase xylD
Query= CharProtDB::CH_024239 (603 letters) >FitnessBrowser__Caulo:CCNA_00862 Length = 591 Score = 183 bits (464), Expect = 2e-50 Identities = 142/446 (31%), Positives = 213/446 (47%), Gaps = 48/446 (10%) Query: 146 DGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLPNKEKV-------RIRQLYA 198 D + CDK P MAA + ++PA+ + GPM G E V R R+ A Sbjct: 120 DAVVLTTGCDKTTPAGIMAATTV-NIPAIVLSGGPMLDGWHENELVGSGTVIWRSRRKLA 178 Query: 199 EGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQLPGSSFVHPDSPLRDALT 258 G++ ++ A+S + G C GTA+T V E +G+ L G + + R + Sbjct: 179 AGEITEEEFIDRAASSAPSAGHCNTMGTASTMNAVAEALGLSLTGCAAIPAPYRERGQMA 238 Query: 259 AAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGSTNHTMHLVAMARAAGIQI 318 +++ + + + + I + ++ N I + A GGSTN H+VAMAR AG++I Sbjct: 239 YKTGQRIVDLAYDDVKPLDI---LTKQAFENAIALVAAAGGSTNAQPHIVAMARHAGVEI 295 Query: 319 NWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRELLKAGLLHEDVNTVAGFGL 378 DD+ D+ PL+ + P G F AGG P ++ ELL+ G LH DV TV G + Sbjct: 296 TADDWRAAYDI-PLIVNMQPAGKYLGERFHRAGGAPAVLWELLQQGRLHGDVLTVTGKTM 354 Query: 379 SRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGTKVLSGNL-GRAVMKTSAV 437 S +G E S D VI + +P + G VL GNL A+MK+S + Sbjct: 355 SENL-------------QGRETS-DREVIFPYHEPLAEKAGFLVLKGNLFDFAIMKSSVI 400 Query: 438 -----------PVENQVIEAPAVVFESQHDVM-----PAFEAGLLDRDCVVVVRHQGPKA 481 P + V EA A+VF+ D PA E +D C++V+R GP Sbjct: 401 GEEFRKRYLSQPGQEGVFEARAIVFDGSDDYHKRINDPALE---IDERCILVIRGAGPIG 457 Query: 482 -NGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD 540 G E+ + PP +L + + DGR SG + PS ++ +PE+ GG L+ +R Sbjct: 458 WPGSAEVVNMQPPDHLLKKGIMSLPTLGDGRQSGTADS-PSILNASPESAIGGGLSWLRT 516 Query: 541 GDIIRVNGQTGELTLLVDEAELAARE 566 GD IR++ TG LVDEA +AAR+ Sbjct: 517 GDTIRIDLNTGRCDALVDEATIAARK 542 Lambda K H 0.318 0.134 0.392 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: 860 Number of extensions: 49 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 603 Length of database: 591 Length adjustment: 37 Effective length of query: 566 Effective length of database: 554 Effective search space: 313564 Effective search space used: 313564 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: 53 (25.0 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