Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate Ac3H11_3523 Xylonate dehydratase (EC 4.2.1.82)
Query= BRENDA::Q9A9Z2 (595 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3523 Length = 593 Score = 939 bits (2428), Expect = 0.0 Identities = 452/590 (76%), Positives = 523/590 (88%), Gaps = 3/590 (0%) Query: 9 TPRR-FRSRDWFDNPDHIDMTALYLERFMNYGITPEELRSGKPIIGIAQTGSDISPCNRI 67 TPRR FRSR+WF P+ DMTALYLERFMNYG+TPEELRSG+PIIGIAQTGSD+SPCNRI Sbjct: 4 TPRRPFRSREWFAAPERSDMTALYLERFMNYGLTPEELRSGRPIIGIAQTGSDLSPCNRI 63 Query: 68 HLDLVQRVRDGIRDAGGIPMEFPVHPIFENCRRPTAALDRNLSYLGLVETLHGYPIDAVV 127 HLDL +RVRDGIRDAGGIPMEFPVHPIFENCRRPTAALDRNL+YLGLVE L+GYPIDAVV Sbjct: 64 HLDLARRVRDGIRDAGGIPMEFPVHPIFENCRRPTAALDRNLAYLGLVEILYGYPIDAVV 123 Query: 128 LTTGCDKTTPAGIMAATTVNIPAIVLSGGPMLDGWHENELVGSGTVIWRSRRKLAAGEIT 187 LTTGCDKTTPAG+MAA+TV+IPAIVLSGGPMLDGWH+ +LVGSGTVIWRSRR+LAAGEI Sbjct: 124 LTTGCDKTTPAGVMAASTVDIPAIVLSGGPMLDGWHDGQLVGSGTVIWRSRRQLAAGEID 183 Query: 188 EEEFIDRAASSAPSAGHCNTMGTASTMNAVAEALGLSLTGCAAIPAPYRERGQMAYKTGQ 247 EEEF+ RA +SAPSAGHCNTMGTASTMNAVAEALGLSL GCAAIPAPYRERGQMAY+TG+ Sbjct: 184 EEEFLQRACNSAPSAGHCNTMGTASTMNAVAEALGLSLPGCAAIPAPYRERGQMAYETGR 243 Query: 248 RIVDLAYDDVKPLDILTKQAFENAIALVAAAGGSTNAQPHIVAMARHAGVEITADDWR-A 306 RIV++AY+D++P ILT+++F NA+++V+ AGGS+NAQ HI+AMARHAGV++TA DW Sbjct: 244 RIVEMAYEDLRPSRILTRESFLNALSVVSVAGGSSNAQVHIMAMARHAGVQLTAQDWTDH 303 Query: 307 AYDIPLIVNMQPAGKYLGERFHRAGGAPAVLWELLQQGRLHGDVLTVTGKTMSENLQGRE 366 AYD+PL++NMQPAG++LGERF RAGG PA++WEL Q G+LH D +VTGKT+ ENLQGRE Sbjct: 304 AYDLPLLLNMQPAGQFLGERFFRAGGVPALMWELQQAGKLHADCASVTGKTVGENLQGRE 363 Query: 367 TSDREVIFPYHEPLAEKAGFLVLKGNLFDFAIMKSSVIGEEFRKRYLSQPGQEGVFEARA 426 T DREVI P+ PL KAGF+VL GNLFDF IMK+SVI E FR+RYLS+PGQEG+FEARA Sbjct: 364 THDREVIRPFSNPLMHKAGFMVLSGNLFDFGIMKTSVISEAFRQRYLSRPGQEGIFEARA 423 Query: 427 IVFDGSDDYHKRINDPALEIDERCILVIRGAGPIGWPGSAEVVNMQPPDHLLKKGIMSLP 486 +VF+G+DDYH RINDPAL IDE CILV+RGAGPIGWPGSAEVVNMQPPD L+K+GI +LP Sbjct: 424 VVFEGADDYHARINDPALNIDEGCILVMRGAGPIGWPGSAEVVNMQPPDALIKRGINTLP 483 Query: 487 TLGDGRQSGTADSPSILNASPESAIGGGLSWLRTGDTIRIDLNTGRCDALVDEATIAARK 546 TLGDGRQSGTADSPSILNASPESA+GGGLSWL++GDT+RIDLNTGRCDALV IA RK Sbjct: 484 TLGDGRQSGTADSPSILNASPESAVGGGLSWLQSGDTVRIDLNTGRCDALVTPEEIARRK 543 Query: 547 QD-GIPAVPATMTPWQEIYRAHASQLDTGGVLEFAVKYQDLAAKLPRHNH 595 +D P VPA+ +PW+ +YR QL G L+FA+ +Q ++ K PRHNH Sbjct: 544 RDLPAPPVPASQSPWEALYREKTGQLADGATLDFALAFQRISEKTPRHNH 593 Lambda K H 0.319 0.136 0.411 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: 1218 Number of extensions: 52 Number of successful extensions: 3 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: 595 Length of database: 593 Length adjustment: 37 Effective length of query: 558 Effective length of database: 556 Effective search space: 310248 Effective search space used: 310248 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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