Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_066328676.1 BLR17_RS00255 bifunctional aspartate kinase/homoserine dehydrogenase I
Query= reanno::Cola:Echvi_2000 (815 letters) >NCBI__GCF_900100165.1:WP_066328676.1 Length = 803 Score = 482 bits (1240), Expect = e-140 Identities = 289/822 (35%), Positives = 480/822 (58%), Gaps = 31/822 (3%) Query: 1 MKIIKFGGSSIANYENIQKVFSIIEQK-SEKEAFALVFSAFGGVTEQLLQCANIAQQSEE 59 MKI+KFGG S++N E I KV SII K ++ E A+V SA G T++L + +A ++ + Sbjct: 1 MKILKFGGKSLSNGEGINKVVSIITDKVNQGEKIAIVVSARGNATDELEEILAVASKNAD 60 Query: 60 SYHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDY 119 Y ++L++ +K QQ A + F L LF G+ LI + S++ D Sbjct: 61 -YKSLLEQFKK-----------YQQDVYANVDLSEEFAVLDKLFEGVSLIGDYSSKIKDQ 108 Query: 120 VLSFGERLSNFILAAGLQAKGIGTSYVDARDLVKTDDRFGHAKVNFKTTNKLIQDHFKSH 179 +LS GE LS +L A L KG+ + D+R +KTD +FG A+ + + K + +FK + Sbjct: 109 ILSIGELLSAKLLTAILVEKGVNARFADSRTFLKTDSKFGDAQPLEQVSKKNVIKYFKDN 168 Query: 180 DD-IKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLV 238 DD + V+TGFIGS TTT+GR+GS+YTAS+ A L A++++ +T V G+ TA+P LV Sbjct: 169 DDAVNVVTGFIGSNINNVTTTLGRNGSNYTASLLANYLDAKELQNYTHVDGIYTANPDLV 228 Query: 239 YTAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRISKDSG 298 A I L++NEA EL++FGA ++ T+ P ++++IP+ I NTF + GT I+ S Sbjct: 229 ADAKKIDHLTFNEANELANFGATILHAKTIIPLLEKNIPLRILNTFNHENEGTLITATSK 288 Query: 299 EGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICVA 358 G IK +S +++++++N++G GL+ GV R F + +N I++ +ISQ SSE I + Sbjct: 289 SGG-IKTLSVLEDLALVNLEGRGLLGKTGVDARIFKVMGDNNISVSIISQGSSERGIGLV 347 Query: 359 IASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQALG 418 +A A++A +E+EF + S ++++I + D++VI+++G+++ R + AL Sbjct: 348 VAESQATKAMIELEKEFENDFYSKDVNKISVTDDVSVISIIGQDL----STFYRPYTALI 403 Query: 419 RNNVNVAAIAQGSSELNISAVITQADLQKALNALH-EAFFLSDYKVLHLFLVGVGLIGKA 477 +N + + N+S V+ +++L KALN +H E F +S K +++ + G GL+G Sbjct: 404 KNKIIPILFNNTVTGKNVSLVVKKSELNKALNVIHGEIFGVS--KKINIAVFGHGLVGGT 461 Query: 478 LTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDKFIG 537 L I + K +++ + + I +ANS+ + ++DG V N + I Sbjct: 462 LINQILESAKAIEKRKDIKLNIFAIANSKNVLLNKDGVSPNWVNEIQTNGFAYTIKDVIA 521 Query: 538 TMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLAGQR 597 E + N + VD TAS + Y ++++ +++ NK AN+ YK+L+K+ + Sbjct: 522 YANENHLENLIAVDNTASAAFVENYIPLVENGFDLISSNKVANTLSYGFYKELRKVLAEN 581 Query: 598 GVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELE-KGMPFSEVVA 656 + YETNV AGLP+I+T++ L LSG+++ +I+ V SG+++Y+F+ K PFS+++ Sbjct: 582 QKNYLYETNVGAGLPLIDTIKLLHLSGENITKIKGVFSGTLSYLFNNFSAKDAPFSDILK 641 Query: 657 QAKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVPEF 716 +A + GYTEPDPR+DL G DV RK+LIL RE FE++ IQ+++PE + S +F Sbjct: 642 EAIDNGYTEPDPREDLCGNDVGRKLLILARELDLQNEFEEIAIQNLIPEHLRE-GSAADF 700 Query: 717 FKKLQKHDGHFQQLLDEANAKGEKLRFMATL------ENGKAKVGLNSLDSEHPFFTLKG 770 KL++ D + ++ +E LR++ L + G +V L S+ S+ LKG Sbjct: 701 LTKLKEFDPIYTKIKEE-QKPNHVLRYIGELSGDLQNDKGILEVKLVSVPSDTALGGLKG 759 Query: 771 SDNMILFTTERYNDFPMIVRGPGAGADVTAAGVFADIIRLGN 812 SD+ TE Y D P++++G GAG+ VTA GVF DI+RL + Sbjct: 760 SDSFFEIYTESYGDRPIVIQGAGAGSAVTARGVFGDILRLSD 801 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: 1471 Number of extensions: 84 Number of successful extensions: 9 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: 803 Length adjustment: 41 Effective length of query: 774 Effective length of database: 762 Effective search space: 589788 Effective search space used: 589788 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)
Align candidate WP_066328676.1 BLR17_RS00255 (bifunctional aspartate kinase/homoserine dehydrogenase I)
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00657.hmm # target sequence database: /tmp/gapView.2438427.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00657 [M=442] Accession: TIGR00657 Description: asp_kinases: aspartate kinase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-99 318.3 7.1 4.9e-99 318.3 7.1 1.4 2 NCBI__GCF_900100165.1:WP_066328676.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100165.1:WP_066328676.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 318.3 7.1 4.9e-99 4.9e-99 5 440 .. 3 441 .. 1 443 [. 0.91 2 ? -4.1 0.1 0.32 0.32 384 417 .. 457 490 .. 456 493 .. 0.82 Alignments for each domain: == domain 1 score: 318.3 bits; conditional E-value: 4.9e-99 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee.keliekirekhlea 76 ++KFGG S+ n+e i+kv+ i++ + ++g++ ++VvSA+++ Td+L e+ +s++++ k+l+e+ ++ + + NCBI__GCF_900100165.1:WP_066328676.1 3 ILKFGGKSLSNGEGINKVVSIITDKVNQGEKIAIVVSARGNATDELEEILAVASKNADyKSLLEQFKKYQQDV 75 79**************************************************999998777777777777776 PP TIGR00657 77 leela.sqalkeklkallekeleevkk.....ereldlilsvGEklSaallaaaleelgvkavsllgaeagil 143 ++++ s+ a+l+k +e v ++ +d ils+GE lSa+ll+a+l e+g ++ + +++ + NCBI__GCF_900100165.1:WP_066328676.1 76 YANVDlSE-----EFAVLDKLFEGVSLigdysSKIKDQILSIGELLSAKLLTAILVEKG-VNARFADSRTFLK 142 66666553.....3344444444444445566***************************.8899********* PP TIGR00657 144 tdsefgrAkvleeikterleklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiyt 214 tds+fg+A+ le+++++++ k+ + + + vv+GFiG++ ++ +ttLGR+GS +tA+llA+ l+A+e++ yt NCBI__GCF_900100165.1:WP_066328676.1 143 TDSKFGDAQPLEQVSKKNVIKYFKDNddAVNVVTGFIGSNINNVTTTLGRNGSNYTASLLANYLDAKELQNYT 215 *******************999999889********************************************* PP TIGR00657 215 DVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivaksk 287 VdGiyta P +v +A+++d+++++Ea ELa++Ga +Lh +t+ p+ +++ip+++ +tfn+e+eGTli+a+sk NCBI__GCF_900100165.1:WP_066328676.1 216 HVDGIYTANPDLVADAKKIDHLTFNEANELANFGATILHAKTIIPLLEKNIPLRILNTFNHENEGTLITATSK 288 ***********************************************************************77 PP TIGR00657 288 seeepavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkake 358 s +k+ls+ ++ alv+++g + g+ a++f+ + +++++v +i+q sse +i +vv +++a ka NCBI__GCF_900100165.1:WP_066328676.1 289 S---GGIKTLSVLEDLALVNLEGRGLLgkTGVDARIFKVMGDNNISVSIISQGSSERGIGLVVAESQATKAMI 358 4...46*******************9999****************************************9999 PP TIGR00657 359 llkkkvkee...kaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis.sseikisvvvdek 427 +l+k+++++ k++++++v+++++++s++G+++++ ++ ++++ i+i + ++s+vv+++ NCBI__GCF_900100165.1:WP_066328676.1 359 ELEKEFENDfysKDVNKISVTDDVSVISIIGQDLST---FYRPYTALIKNKIIPILFNNtVTGKNVSLVVKKS 428 999888875333788899*****************9...555555666667788888778899********** PP TIGR00657 428 daekavealhekl 440 + +ka++++h ++ NCBI__GCF_900100165.1:WP_066328676.1 429 ELNKALNVIHGEI 441 **********876 PP == domain 2 score: -4.1 bits; conditional E-value: 0.32 TIGR00657 384 lvGagmksapgvaakifeaLaeeniniemissse 417 lvG +++++ ak++e+ ++ ++ni +i+ s NCBI__GCF_900100165.1:WP_066328676.1 457 LVGGTLINQILESAKAIEKRKDIKLNIFAIANSK 490 6888888888999999999999999999998764 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (803 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 46.60 // [ok]
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