Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate GFF835 Psest_0849 6-phosphogluconate dehydratase
Query= BRENDA::P39358 (655 letters) >FitnessBrowser__psRCH2:GFF835 Length = 608 Score = 167 bits (424), Expect = 1e-45 Identities = 149/480 (31%), Positives = 226/480 (47%), Gaps = 47/480 (9%) Query: 119 CDGRTQGTTGMFDSLPYRNDASMVMR-RLIRSLPDAKAVIGVASCDKGLPATMMALAAQH 177 CDG TQG GM ++ R +M L +L DA ++G+ CDK +P ++ Sbjct: 112 CDGVTQGEPGMELAIASREVIAMSTAVALSHNLFDAALLLGI--CDKIVPGLLIGALRFG 169 Query: 178 NIATVLVPGGATLPAKDGEDNGKVQTIGARFANGELSLQDARRAGCKACASSGGGCQFLG 237 ++ V VP G P G N + R+A G+ S + A +A S G C F G Sbjct: 170 HLPAVFVPAG---PMPSGLANKDKAAVRQRYAEGKASRDELLAAEMQAYHSPGT-CTFYG 225 Query: 238 TAGTSQVVAEGLGLAIPHSALAPSGEPVWREIARASARAALNLSQKG---ITTREILTDK 294 TA T+Q++ E +GL +P S+ G P+ + +AR L+ +G E++ ++ Sbjct: 226 TANTNQMLMEVMGLHLPGSSFVNPGTPLRDALTAEAARQVTRLTPQGGCFTPLGELVDER 285 Query: 295 AIENAMTVHAAFGGSTNLLLHIPAIAHQAGCHIPTVDDWIRINKRVPRLVSVLPNGPVYH 354 + NA+ A GGSTN LH+PAIA AG + T D ++ VP L V PNGP Sbjct: 286 VLVNAIVALHATGGSTNHTLHMPAIAQAAGIQL-TWQDMADLSAVVPTLARVYPNGPA-- 342 Query: 355 PTVNAF-MAGGVPEVMLHLRSLGLLHEDVMTVTGSTLKENLDWWEHSERRQRFKQLLLDQ 413 +N F AGGV ++ L + GLLHEDV TV G L + + + + Sbjct: 343 -DINHFHAAGGVAVLVRELLAAGLLHEDVHTVMG----RGLSRYTQEPFLEGGRLTWREG 397 Query: 414 EQINADEVIMSPQQAKARGLTSTITFPVGNIAPEGSVIKSTAIDPSMIDEQGIYYHKGV- 472 + DE ++ P A+ + GN+ V+K +A+ P H+ V Sbjct: 398 AAASLDESLLRP-VARPFSAEGGLRVMSGNLG--RGVMKVSAVAPE---------HRVVE 445 Query: 473 --AKVYLSEKSAIYDIKHDKIKAGDILVIIGVGPSGTGMEETYQVTSALKHL-SYGKHVS 529 A+V+ + + K +++ + V+ GP GM E +++T L L G V+ Sbjct: 446 APARVFADQLELVEAFKAGELERDVVAVVRFQGPRANGMPELHKLTPYLGLLQDRGFKVA 505 Query: 530 LITDARFSGVS--TGACIGHVGPEALAGGPIGKLRTGDL---------IEIKIDCRELHG 578 L+TD R SG S A I HV PEA+ GGP+ ++R GDL +E+ +D EL G Sbjct: 506 LVTDGRMSGASGKVPAAI-HVCPEAIDGGPLARVRDGDLLRVDGQAGVLEVLVDAAELAG 564 Lambda K H 0.317 0.135 0.400 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: 951 Number of extensions: 51 Number of successful extensions: 9 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: 655 Length of database: 608 Length adjustment: 38 Effective length of query: 617 Effective length of database: 570 Effective search space: 351690 Effective search space used: 351690 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: 54 (25.4 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