Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate BPHYT_RS21270 BPHYT_RS21270 dihydroxy-acid dehydratase
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >FitnessBrowser__BFirm:BPHYT_RS21270 Length = 586 Score = 590 bits (1521), Expect = e-173 Identities = 300/571 (52%), Positives = 407/571 (71%), Gaps = 10/571 (1%) Query: 8 KKP--LRSQAWFGLKDRDGFLHRSWMKNQGIPHDEFDGRPVIGICNTWSELTPCNAHFRE 65 KKP LRS W+G+ D F HRS G +E+ G+PVI I NTWSE+ C+ HF++ Sbjct: 5 KKPEELRSHRWYGVNDLRSFGHRSRTAQMGYDREEYAGKPVIAILNTWSEINACHTHFKQ 64 Query: 66 LAEYVKKGVHEAGGLPLEFPVMSLGETNLRPTAMLFRNLASMDVEESIRGNPMDGVILLV 125 E VK+G+ +AGG P+E PV +L E +PT ML+RN +M+ EE++R P DGV+L+ Sbjct: 65 RVEEVKRGIWQAGGFPVELPVQTLSEPFQKPTTMLYRNFLAMEAEETLRSYPADGVVLMG 124 Query: 126 GCDKTTPALLMGAASCNLPALAVSGGPMLNGRFRGKNIGSGTGVWQMSEEVRAGTMTQEE 185 GCDKTTP LLMGA S +LPA+ + GPML G + G +GSG+ VW+ E+RAGT+TQ++ Sbjct: 125 GCDKTTPGLLMGAISMDLPAIFLPAGPMLRGNWNGVTLGSGSDVWKYWAELRAGTITQDD 184 Query: 186 FTEAESCMNRSRGHCMTMGTASTMASMVESLGMGLPHNAAIPAVDARRQVLAHLAGRRIV 245 + E + RS GHCMTMGTASTM S E+LG LP A+IPA D+R +A G+RIV Sbjct: 185 WQGIEGGIARSPGHCMTMGTASTMTSAAEALGFTLPGFASIPAADSRHAQMAAKTGKRIV 244 Query: 246 DMVREDLTMDKILTRQAFENAIRTNAAIGGSTNAVVHLIALAKRIGVELSLEDW-ELGSN 304 +MV EDL ++T + +NA+ T A+ GSTNA+VH+IALA+R G+EL+L+ + ++ Sbjct: 245 EMVWEDLKPSDLITAGSVDNAVTTCLALSGSTNAIVHMIALARRAGIELTLDRYDDIARR 304 Query: 305 VPCLVNLQPSGEYLMEDFYYAGGLPAVLKQLGEQGLLHKEALTVNGKTLWDNVRNAANYD 364 P L N++P+G YLMEDF+YAGGL A+L +LGE L+ + TVNG+TL +N+ A ++ Sbjct: 305 TPVLANVRPTGAYLMEDFFYAGGLRALLAELGE--LIDRSQKTVNGRTLGENLEGAEIFN 362 Query: 365 EKVITTFAEPFKPKAGIAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELHAKI 424 + VI +P P +G+AVL+GN+AP+GAVIKP AA LL H GRAVVF++ ++ A+I Sbjct: 363 DDVIRRRDKPLLPNSGLAVLRGNIAPDGAVIKPGAAEPHLLVHTGRAVVFKDYNDMAARI 422 Query: 425 DDESLDIDEHCIMVLKGAGPKGYPGFAEVGNMPLPKKVLQKGITDMVRISDGRMSGTAYG 484 DD++LDIDE+ ++VL+ AGP G PG E G +P+P+K+LQKG+ DMVRISD RMSGT+YG Sbjct: 423 DDDTLDIDENSLIVLQHAGPVGAPGMPEWGQLPIPRKLLQKGVRDMVRISDARMSGTSYG 482 Query: 485 AVVLHVSPEAAAGGPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAAWQAPEAPK--R 542 A VLHV+PE+ GGP A V++GDMIELDV R+L+L VTD+ELARR+AAW P AP+ R Sbjct: 483 ACVLHVAPESFIGGPFALVESGDMIELDVPRRKLNLLVTDDELARRKAAWVRP-APRFTR 541 Query: 543 GYYKLYVEHVLQADQGADLDFLV--GSSGAP 571 GY ++ HV+QA+QG D DFL G+ AP Sbjct: 542 GYGAMHQVHVMQANQGCDFDFLQRGGAQAAP 572 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: 982 Number of extensions: 41 Number of successful extensions: 4 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: 577 Length of database: 586 Length adjustment: 36 Effective length of query: 541 Effective length of database: 550 Effective search space: 297550 Effective search space used: 297550 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