Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_012467218.1 CLIM_RS11700 bifunctional aspartate kinase/homoserine dehydrogenase I
Query= reanno::Cola:Echvi_2000 (815 letters) >NCBI__GCF_000020465.1:WP_012467218.1 Length = 822 Score = 679 bits (1751), Expect = 0.0 Identities = 364/821 (44%), Positives = 523/821 (63%), Gaps = 9/821 (1%) Query: 1 MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60 MKI KFGGSS+ + I+K+ II + + +V SAF VT+ LL+ AN+A E Sbjct: 1 MKIYKFGGSSLGSAARIKKIAGIIRSGLQPDCPVVVVSAFHRVTDLLLEAANVACTGREG 60 Query: 61 YHTILQELEKRHLEIVKKLVPVQQQSTALT-FVKVRFNELGDLFHGIYLIKECSNRTMDY 119 Y IL ++ + H ++ L L+ ++V EL DL HG++L++E S ++ Sbjct: 61 YLRILDDIGQLHKTVLDGLFSGSDAYAGLSDSIRVELAELHDLLHGVFLLRELSEKSTAL 120 Query: 120 VLSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSH 179 +LSFGERLS I+A L + Y+DAR+L+ TD +G A V+ + T + I + Sbjct: 121 LLSFGERLSARIVAGYLNLLKLPAVYLDARELIVTDANYGSATVDLEETFQRIVNAPVPD 180 Query: 180 DDIKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLVY 239 I V+TG+I + G TTT+GR GSDYTAS+F AALGAE++ IWTDV G +ADP+ V Sbjct: 181 GVIPVVTGYIAAAGDGTTTTLGRGGSDYTASLFGAALGAEEIFIWTDVDGFFSADPKRVR 240 Query: 240 TAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDSGE 299 A +P +SY EAMELSH GAKV+ P T+ PAMK IP+ IKN+F PD GTRI ++ Sbjct: 241 DARVLPFISYAEAMELSHAGAKVLHPFTILPAMKASIPVLIKNSFNPDAPGTRIERELDP 300 Query: 300 GKI-----IKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHS 354 + + G+SS++++ +LN+ G G+V V G++ R F LA + IN+I ISQASSE S Sbjct: 301 VAVRQIHPVTGLSSINSVVLLNLSGSGMVGVPGIASRLFSCLAKHHINVIFISQASSEQS 360 Query: 355 ICVAIASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMF 414 I +AI A++A ++E+EF E+Q+ +D + + +A++AVVG NM +PG S ++F Sbjct: 361 ISLAINPAQAAKANRILEDEFAAEMQARLIDPLVLRRHLALVAVVGNNMSGHPGVSAQLF 420 Query: 415 QALGRNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLI 474 + LG+N +NV A+AQG++E+NIS VI D KALN +HE+FFLS KV H+FL G G I Sbjct: 421 ETLGKNGINVIAVAQGANEMNISVVIDNRDEDKALNCIHESFFLSQRKV-HVFLAGTGTI 479 Query: 475 GKALTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEP--MDM 532 K+L + I + NL+ E LD+ + G+AN+R + ++G DL + EP + Sbjct: 480 AKSLIRQISRHRMNLRREKDLDVLVCGLANTRRIAHADEGIDLDRWEDALKPREPGYAGI 539 Query: 533 DKFIGTMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKK 592 + +I + E N N+VFVDCTAS +VA+ Y ++L + + +VT NK +G E Y++++ Sbjct: 540 EGYIRLIRERNLHNTVFVDCTASGNVAEQYPELLRANISVVTANKLGMAGCAELYEQIRT 599 Query: 593 LAGQRGVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFS 652 RF YETNV AGLP+INTL DL SGD++ IE VLSG++++IF+EL KG FS Sbjct: 600 AQRVSNARFLYETNVGAGLPIINTLNDLKNSGDNIISIEGVLSGTLSFIFNELRKGGRFS 659 Query: 653 EVVAQAKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAAS 712 ++V AKE GYTEPDPRDDLSG D ARK+LILGRE G + + DVE +S+VPE+ Sbjct: 660 DIVRMAKEAGYTEPDPRDDLSGADFARKVLILGRELGCPMIYSDVECESLVPEELRGEMP 719 Query: 713 VPEFFKKLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSD 772 V EF +L D + + + A G + + + +GKA +G+ + P L GS+ Sbjct: 720 VEEFLGRLSSVDRWYAEEIQTAGKAGMTIAYAGEIRDGKASIGVKRVPLSSPIAGLNGSE 779 Query: 773 NMILFTTERYNDFPMIVRGPGAGADVTAAGVFADIIRLGNY 813 NM++FTT+RYN P++VRGPGAG +VTA GVFADI+R+ +Y Sbjct: 780 NMVVFTTDRYNITPLVVRGPGAGGEVTAGGVFADILRIASY 820 Lambda K H 0.317 0.134 0.375 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: 1397 Number of extensions: 64 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: 815 Length of database: 822 Length adjustment: 41 Effective length of query: 774 Effective length of database: 781 Effective search space: 604494 Effective search space used: 604494 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: 56 (26.2 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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