Align L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 (characterized)
to candidate Ac3H11_2082 Phosphogluconate dehydratase (EC 4.2.1.12)
Query= SwissProt::Q1JUQ1 (583 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2082 Length = 589 Score = 189 bits (480), Expect = 3e-52 Identities = 158/517 (30%), Positives = 249/517 (48%), Gaps = 32/517 (6%) Query: 42 PIIGICNTWSELTPCNAHFRKLA-----EHVKRG--ISEAGGFPVEFPVFSNGESNLRPS 94 P IG+ ++++ + ++ E K+G + AGG P + G + S Sbjct: 66 PNIGVVTAYNDMLSAHQPYQSYPAVLRDEAAKQGATVQVAGGVPAMCDGVTQGTPGMELS 125 Query: 95 AMLTRNLASMDVEEAIRGNPIDAVVLLAGCDKTTPALLMGAASCD-VPAIVVSGGPMLNG 153 + +R+ +M A+ + D +LL CDK P LL+GA +P + V GPM G Sbjct: 126 -LFSRDAIAMATAVALSHDVFDGALLLGVCDKIVPGLLIGALHYGHLPCVFVPAGPMGTG 184 Query: 154 KLEGKNIGSGTAVWQLHEALKAGEIDVHHFLSAEAGMSRSAGTCNTMGTASTMACMAEAL 213 L K+ ++ E G + L AE+ S GTC GTA++ + EA+ Sbjct: 185 -LSNKDKA------KVREQYAQGLVGRDELLQAESAAYHSPGTCTFYGTANSNQMLLEAM 237 Query: 214 GVALPHNA-AIPAVDSRRYVL--AHMSGIRIVEMALEGLVLSKILTRAAFENAIRANAAI 270 G+ +P A P ++R A + + I + + + K++ NA+ A A Sbjct: 238 GLHVPGAAFESPGTEAREAFTRQALRTVLDIGKRSKRFTPIGKLVDERCIVNAMAALLAT 297 Query: 271 GGSTNAVIHLKAIAGRIGVPLELEDWMRIGRDTPTIVDLMPSGRFPMEEFYYAGGLPAVL 330 GGSTN +IH AIA G+ ++ D+ + P + + P+G + +F AGG P +L Sbjct: 298 GGSTNHLIHWVAIARSAGILIDWTDFDELSSVVPLLARVYPNGDADVNQFQAAGGPPWIL 357 Query: 331 RRLGEGGLLPNPDALTVNGKSLWDNVREAP--NYDEEVIRPLDRPLIADGGIRILRGNLA 388 R L GG + +PD ++VN + D + AP + D V+RP+ P GG+R+L+G L Sbjct: 358 RELLAGGFM-HPDVMSVNVGGIADGGKSAPAVSGDTSVLRPVSAPFSPTGGLRLLQGRLG 416 Query: 389 PRGAVLKPSAASPELLKHRGRAVVFENLDHYKATINDEALDIDASSVMVLKNCGPRGYPG 448 AV+K SA + A VF++ + A + A D++ V V++ GP+ G Sbjct: 417 --RAVIKVSAVPEDRHIIEAPARVFDSQEALLAAFS--AGDVNQDMVAVVRFQGPQA-NG 471 Query: 449 MAEVGNMGLPPKLLRQGVKDMVRISDARMSGTAYGTV--VLHVAPEAAAGGPLAAVRNGD 506 M E+ + P +L+ + ++D RMSG A G V +HV PEA AGGPLA VR+GD Sbjct: 472 MPELHKLTPPLAVLQNQGFKVALVTDGRMSG-ASGKVPAAIHVTPEALAGGPLAKVRDGD 530 Query: 507 WIELDCEAGTLHLDITDDELHRRLSDVDPTAAPGVAG 543 + +D AGT LD+ DE P +AP G Sbjct: 531 IVRVDAVAGT--LDVLVDEATWAARTPSPYSAPAQTG 565 Lambda K H 0.319 0.136 0.412 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: 866 Number of extensions: 54 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: 583 Length of database: 589 Length adjustment: 37 Effective length of query: 546 Effective length of database: 552 Effective search space: 301392 Effective search space used: 301392 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