Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate Synpcc7942_1001 Synpcc7942_1001 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >FitnessBrowser__SynE:Synpcc7942_1001 Length = 616 Score = 304 bits (779), Expect = 8e-87 Identities = 170/415 (40%), Positives = 259/415 (62%), Gaps = 17/415 (4%) Query: 339 SVVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELAKTIDENP 398 +++V K+GG ++ VE++ VA++I + +G + VVV+SAMG +TD L++LA I NP Sbjct: 21 ALIVQKYGGTSVGSVERITAVAQRIAQTVAAGNQVVVVVSAMGHSTDELLKLANAISANP 80 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKAISFTGNQLKIITDKRYGSARIIDINTDII 458 RELD+LL+TGE S+AL+S+AL ++G AIS TG Q+ IIT+ + ARI++I+ + Sbjct: 81 SRRELDMLLATGEQVSIALLSMALHEQGCDAISMTGAQVGIITEAHHSRARILEIDPQRL 140 Query: 459 SRYLKQDFIPVVAGFQGI-----TETGDITTLGRGGSDLTAIALAYSLGADLCELYKDVD 513 L + VVAGFQGI T +ITTLGRGGSD +A+ALA +L AD CE+Y DV Sbjct: 141 QSQLDAGRVVVVAGFQGIASSDRTALTEITTLGRGGSDTSAVALAAALNADRCEIYTDVP 200 Query: 514 GVYTADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKETR 573 G+ T DPR+V +A +++E++ +EM+EL+ GA VL RA E AR YGV+++++++ + Sbjct: 201 GILTTDPRLVPEAHLLEEITCDEMLELASLGASVLHPRAVEIARNYGVRLVVRSSWTQEP 260 Query: 574 GTLI----------WEGTKVENPIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMG 623 GT + +G ++ P V + + AKV L VPD+PG+AA + ++Q G Sbjct: 261 GTGVVAPPRRSDRSLQGLEIGRP-VDGLALDTDQAKVALLHVPDRPGIAASLFGEMAQRG 319 Query: 624 VNIDMIIQGMKSGEYNTVAFIVPESQLGKLDIDLLKTRSE-AKEIIIEKGLAKVSIVGVN 682 VN+D+IIQ + G N ++F V ++ L K + + ++ E E +AKVSI GV Sbjct: 320 VNVDLIIQSIHEGNSNDISFTVSQADLEKAEAGTTQLLADLGGEQQSEAAVAKVSISGVG 379 Query: 683 LTSTPEISATLFETLANEGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFELD 737 + P I+A +F LA GINI MIS S ++S +I + A+ A+ FEL+ Sbjct: 380 IVGRPGIAAQMFSALAQGGINIQMISTSEVKVSCVIAAADQQRAIAALQESFELE 434 Score = 89.4 bits (220), Expect = 5e-22 Identities = 52/157 (33%), Positives = 83/157 (52%), Gaps = 6/157 (3%) Query: 586 PIVRAVTFEDGMAKVVLKDVPDKPGVAARIMRTLSQMGVNIDMIIQGMKSGEYNTVAFIV 645 P VR V + A++ + +VPD PG+AA I + L+ +++DMIIQ + +N Sbjct: 450 PAVRGVALDRDQARLAILNVPDLPGMAATIFQILADRQISVDMIIQSQRGRIHNGQPCRD 509 Query: 646 PESQLGKLDIDLLKTRSEAK------EIIIEKGLAKVSIVGVNLTSTPEISATLFETLAN 699 L D +L +A + I+ +AKVSIVG + P ++A +F LAN Sbjct: 510 IACTLPPADAELAAAALQAFADQHGCSLEIQTEIAKVSIVGSGMVQQPGVAAQMFAALAN 569 Query: 700 EGINIDMISASSSRISVIIDGKYVEDAVKAIHSRFEL 736 GINI MI+ S ++S I+D +A++ +H+ F L Sbjct: 570 HGINIHMIATSEIKVSCIVDASQAVEALQTVHAAFGL 606 Lambda K H 0.318 0.137 0.377 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: 839 Number of extensions: 32 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 739 Length of database: 616 Length adjustment: 39 Effective length of query: 700 Effective length of database: 577 Effective search space: 403900 Effective search space used: 403900 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 Apr 09 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