Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_012114021.1 XAUT_RS10055 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000017645.1:WP_012114021.1 Length = 604 Score = 296 bits (758), Expect = 2e-84 Identities = 199/559 (35%), Positives = 301/559 (53%), Gaps = 46/559 (8%) Query: 23 GLTDDDFE--KPFIGIANSYTDIVPGHIHLRELAEAVKEGVNAAGGVAFEFNTMAICDGI 80 GLT ++ + KP IGIA + +D+ P + H +LA+ V++G+ A GGV FEF I + Sbjct: 41 GLTREELQSGKPIIGIAQTGSDLSPCNRHHLDLAKRVRDGIEAMGGVPFEFPVHPIQETG 100 Query: 81 AMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCDKIVPGMLMAAARLDIPAIVV 140 + +LA +V + + LDG+VL CDK P +MAAA ++IPAIV+ Sbjct: 101 KRPTAALDRNLAYLGLV-----EILYGYPLDGVVLTTGCDKTTPACIMAAATVNIPAIVL 155 Query: 141 TGGPMLPGEFKGRKVDLINVYEGVGTV--------SAGEMSEDELEELERCACPGPRSCA 192 +GGPML G +KG + G GTV +AGE+ +E ++ + P C Sbjct: 156 SGGPMLNGWWKGERT-------GSGTVVWKNRERFAAGEIDYNEFMDVVASSAPSVGHCN 208 Query: 193 GLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMVQENLKPTMIMSQE 252 + TA+TM L EALGMSLPGCA A + QIA +GKRIV+MV E+LKP+ I+++E Sbjct: 209 TMGTASTMNALAEALGMSLPGCAAIPAPYRERGQIAYDTGKRIVDMVWEDLKPSDILTRE 268 Query: 253 AFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIPHIASISPAGEHMM 312 AFENA+ V+ A+GGSTN +H+ AIA + G+ +N+D + + IP + ++ PAGE++ Sbjct: 269 AFENAIRVNSAIGGSTNAPIHLNAIARHV-GVPLNVDDWQAVGHKIPLLVNLQPAGEYLG 327 Query: 313 LDLDRAGGIPAVLKTL--EDHINRECVTCTGRTVQENIENVKVGHRDVIRPLDSPVHSEG 370 + RAGG+PAV+ L + I+ +T GR++ EN + R+VI+ D+P+ + Sbjct: 328 EEFHRAGGVPAVVAELIEKGKIHEGALTVNGRSIGENCKGKLSWDREVIKTYDAPLKEDA 387 Query: 371 GLAILRGNLAPRGSVVKQGAVA-----------EDMMVHEGPAKVFNSEDECMEAIFGGR 419 G +L GNL +V+K ++ D EG A VF ++ I Sbjct: 388 GFIVLHGNLF-NNAVMKTSVISPEFRDRFLSNPNDPEAFEGRAVVFEGPEDYHHRIDDPS 446 Query: 420 --IDEGDVIVIRYEGPKGGPGMREMLN--PTSAIAGMGLERVALITDGRFSGGTRGPCVG 475 IDE ++ IR GP G PG E++N P +A+ G+ + I DGR SG + P + Sbjct: 447 LGIDEYTLLFIRGTGPLGYPGGAEVVNMQPPTALIKKGIHALPCIGDGRQSGTSGSPSIL 506 Query: 476 HVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERL-----QSAVKPRRSVKG 530 + SPEA G LA + GD +RID+ + ++ +SP E+ +R +S Sbjct: 507 NASPEAAAGGGLALLKTGDRVRIDLNTCTADILISPEELAQRRADLQGHGGFPMPQSQTP 566 Query: 531 WLARYRKLAGSADTGAVLR 549 W R + D G VL+ Sbjct: 567 WQEIQRSMVAQFDEGMVLK 585 Lambda K H 0.319 0.136 0.397 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: 853 Number of extensions: 34 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: 549 Length of database: 604 Length adjustment: 36 Effective length of query: 513 Effective length of database: 568 Effective search space: 291384 Effective search space used: 291384 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 Apr 10 2024. The underlying query database was built on Apr 09 2024.
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