Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_055435097.1 ASC41_RS02630 bifunctional aspartate kinase/homoserine dehydrogenase I
Query= reanno::Cola:Echvi_2000 (815 letters) >NCBI__GCF_001418085.1:WP_055435097.1 Length = 1131 Score = 472 bits (1214), Expect = e-137 Identities = 294/826 (35%), Positives = 480/826 (58%), Gaps = 42/826 (5%) Query: 1 MKIIKFGGSSIANYENIQKVFSIIEQKSE-KEAFALVFSAFGGVTEQLLQCANIAQQSEE 59 MKI+KFGG S+AN E + +V SIIE K + +E A+V SA G T+QL A + +E Sbjct: 327 MKILKFGGKSLANGEGLNRVISIIENKVKAEENIAVVVSARGKATDQLESILEKAVK-DE 385 Query: 60 SYHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDY 119 +Y T + Q+ T + + F L LF G+ L+ + S + D Sbjct: 386 AYATDFDAFKN------------DQKGTIVVDFETEFLRLESLFAGVQLLGDYSPKIKDE 433 Query: 120 VLSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSH 179 VL+ GE +S ++ L K I DAR +KTDD FG+AK + K + +FK + Sbjct: 434 VLAQGELISAKLITGLLVDKNINAKVADARTFIKTDDTFGNAKPIDALSKKNVVAYFKQN 493 Query: 180 DD--IKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRL 237 + + ++TGFI S +TTT+GR+GS+YTA++ A L AE+++ +T V+G+ TA+P L Sbjct: 494 NGTTVNIVTGFIASNRDNKTTTLGRNGSNYTAALLANYLDAEELQNYTHVNGIYTANPDL 553 Query: 238 VYTAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDS 297 V A I +LS+ EA EL++FG ++ T+ P ++++IP+ I NTF P++ GT I+ + Sbjct: 554 VADAIKIERLSFTEANELANFGTTILHAKTIIPLIEKNIPLRILNTFNPEDKGTIITAQN 613 Query: 298 GEGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICV 357 + K I+ +S +DN++++N++G GL+ VGV R F L+ I++ +ISQ SSE I + Sbjct: 614 -KDKGIRSLSVLDNVALVNIEGRGLLGKVGVDARIFTALSKENISVSIISQGSSERGIGL 672 Query: 358 AIASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQ--HNPGASGRMFQ 415 I ++ A+RA V+E+EF + S ++++I ++ D++VI+++G+ + H P F Sbjct: 673 VIEAEHANRAVIVLEQEFENDFYSQDINKISVIDDVSVISIIGQELSTFHKP------FN 726 Query: 416 ALGRNNVNVAAIAQGSSELNISAVITQADLQKALNALH-EAFFLSDYKVLHLFLVGVGLI 474 L +N + + N+S V+ + +L KA+N +H E F +S K ++L + G GL+ Sbjct: 727 NLIKNQIIPILFNNTITGENVSIVVKKKELHKAVNVIHGEIFGIS--KKINLAIFGHGLV 784 Query: 475 GKALTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDK 534 G AL I K++++ + + I +ANS+ F ++G D + N E ++ Sbjct: 785 GGALVNQIIASAKDIEKRKGIKLNIFAIANSQKALFSKNGIDENWKNTLETNGENYKIED 844 Query: 535 FIGTMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLA 594 + + N + +D T+S + Y ++++ +V+ NK AN+ LE Y +L+ Sbjct: 845 VFQFAKDNHLENLIAIDNTSSLEFVSNYIKLVEQGFDLVSSNKIANTIDLEFYNELRNTL 904 Query: 595 GQRGVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSEL-EKGMPFSE 653 + + YETNV AGLP+I+T++ L LSG+++ RI V SGS++Y+F+ + F+ Sbjct: 905 EKHQKSYLYETNVGAGLPLIDTIKLLHLSGENIVRIRGVFSGSLSYLFNTFSSEDTSFAT 964 Query: 654 VVAQAKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFE--DVEIQSMVPEDCEDAA 711 V+ QA +KG+TEP+PR+DLSG DVARK+LIL RE DLH E DV I++++PE + Sbjct: 965 VLQQALDKGFTEPNPREDLSGNDVARKLLILAREL--DLHNEIGDVTIENLIPEPLRE-I 1021 Query: 712 SVPEFFKKLQKHDGHFQQLLDEANAKGEKLRFMATL------ENG-KAKVGLNSLDSEHP 764 +F L + + FQ+ + EA +G LR++ L ENG + V L S+ S+ P Sbjct: 1022 ETSQFLDSLDEMNTVFQK-IKEAQKEGHVLRYIGDLHGDLSQENGAQLDVKLESVPSQSP 1080 Query: 765 FFTLKGSDNMILFTTERYNDFPMIVRGPGAGADVTAAGVFADIIRL 810 L+G+D++ TE Y + P++++G GAGA VTA GVF DI+RL Sbjct: 1081 LGALQGADSIFEIYTESYGEKPIVIQGAGAGASVTARGVFGDILRL 1126 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: 2042 Number of extensions: 96 Number of successful extensions: 12 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: 1131 Length adjustment: 44 Effective length of query: 771 Effective length of database: 1087 Effective search space: 838077 Effective search space used: 838077 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: 57 (26.6 bits)
This GapMind analysis is from Jul 26 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