Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate N515DRAFT_4002 N515DRAFT_4002 aspartate kinase
Query= reanno::Dyella79:N515DRAFT_4002 (853 letters) >FitnessBrowser__Dyella79:N515DRAFT_4002 Length = 853 Score = 1678 bits (4345), Expect = 0.0 Identities = 853/853 (100%), Positives = 853/853 (100%) Query: 1 MKFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQEDKGKRVEA 60 MKFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQEDKGKRVEA Sbjct: 1 MKFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQEDKGKRVEA 60 Query: 61 ARAIAQRHYDLLDHMQLAVPATLAERLSELAMLAEDGPGAMGELAWAALVQAHGELMSSA 120 ARAIAQRHYDLLDHMQLAVPATLAERLSELAMLAEDGPGAMGELAWAALVQAHGELMSSA Sbjct: 61 ARAIAQRHYDLLDHMQLAVPATLAERLSELAMLAEDGPGAMGELAWAALVQAHGELMSSA 120 Query: 121 LGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPALNARLAELGEVF 180 LGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPALNARLAELGEVF Sbjct: 121 LGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPALNARLAELGEVF 180 Query: 181 ITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQVPGARL 240 ITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQVPGARL Sbjct: 181 ITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQVPGARL 240 Query: 241 LQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIGPEVREHAPS 300 LQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIGPEVREHAPS Sbjct: 241 LQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIGPEVREHAPS 300 Query: 301 VKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETNVTVSLDPTEN 360 VKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETNVTVSLDPTEN Sbjct: 301 VKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETNVTVSLDPTEN 360 Query: 361 LLDSDAIAALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLSGVLAEFGQIRVHLISQ 420 LLDSDAIAALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLSGVLAEFGQIRVHLISQ Sbjct: 361 LLDSDAIAALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLSGVLAEFGQIRVHLISQ 420 Query: 421 SSNNLNLTFVVDENVVDDLLPHLHELLIAAGALRTDDSALFGPSWQALYGSGEVAAPAAS 480 SSNNLNLTFVVDENVVDDLLPHLHELLIAAGALRTDDSALFGPSWQALYGSGEVAAPAAS Sbjct: 421 SSNNLNLTFVVDENVVDDLLPHLHELLIAAGALRTDDSALFGPSWQALYGSGEVAAPAAS 480 Query: 481 WWRTAERERLLRLGAERTPRYVYHLPTVRQQARELKSLGAVDRLHYAVKANTHPAILKAL 540 WWRTAERERLLRLGAERTPRYVYHLPTVRQQARELKSLGAVDRLHYAVKANTHPAILKAL Sbjct: 481 WWRTAERERLLRLGAERTPRYVYHLPTVRQQARELKSLGAVDRLHYAVKANTHPAILKAL 540 Query: 541 AEEGFGFECVSPGELKAVLAAVPESAPLLFTPNFAPRADYEWALTTRATISLDALYQLEN 600 AEEGFGFECVSPGELKAVLAAVPESAPLLFTPNFAPRADYEWALTTRATISLDALYQLEN Sbjct: 541 AEEGFGFECVSPGELKAVLAAVPESAPLLFTPNFAPRADYEWALTTRATISLDALYQLEN 600 Query: 601 WGELFRGREIVLRVDLGRGLGHHEKVRTGGSGSKFGLPVELVDSFLRLADAHGVIVRGLH 660 WGELFRGREIVLRVDLGRGLGHHEKVRTGGSGSKFGLPVELVDSFLRLADAHGVIVRGLH Sbjct: 601 WGELFRGREIVLRVDLGRGLGHHEKVRTGGSGSKFGLPVELVDSFLRLADAHGVIVRGLH 660 Query: 661 AHLGSGILDEGHWGEVYGQLASLAERIGSVAFLDIGGGLGVPSHPGEARLDIAALDRVLR 720 AHLGSGILDEGHWGEVYGQLASLAERIGSVAFLDIGGGLGVPSHPGEARLDIAALDRVLR Sbjct: 661 AHLGSGILDEGHWGEVYGQLASLAERIGSVAFLDIGGGLGVPSHPGEARLDIAALDRVLR 720 Query: 721 SVKAAYPHYQLWMEPGRYLVADAGVLLARVTQQKGKGSWRYLGVDTGMNSLIRPALYEAW 780 SVKAAYPHYQLWMEPGRYLVADAGVLLARVTQQKGKGSWRYLGVDTGMNSLIRPALYEAW Sbjct: 721 SVKAAYPHYQLWMEPGRYLVADAGVLLARVTQQKGKGSWRYLGVDTGMNSLIRPALYEAW 780 Query: 781 HEIVNLTRLDEPATGLFQVVGPICESGDVLGTDRRLPEAQEGDVVLVAQAGAYGKVMSSP 840 HEIVNLTRLDEPATGLFQVVGPICESGDVLGTDRRLPEAQEGDVVLVAQAGAYGKVMSSP Sbjct: 781 HEIVNLTRLDEPATGLFQVVGPICESGDVLGTDRRLPEAQEGDVVLVAQAGAYGKVMSSP 840 Query: 841 YNMRDEAEEVILD 853 YNMRDEAEEVILD Sbjct: 841 YNMRDEAEEVILD 853 Lambda K H 0.319 0.135 0.398 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: 2350 Number of extensions: 90 Number of successful extensions: 1 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: 853 Length of database: 853 Length adjustment: 42 Effective length of query: 811 Effective length of database: 811 Effective search space: 657721 Effective search space used: 657721 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 (21.8 bits) S2: 56 (26.2 bits)
Align candidate N515DRAFT_4002 N515DRAFT_4002 (aspartate kinase)
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.8556.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-96 310.2 0.0 1.7e-96 309.9 0.0 1.1 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_4002 N515DRAFT_4002 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_4002 N515DRAFT_4002 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 309.9 0.0 1.7e-96 1.7e-96 6 441 .. 1 448 [. 1 449 [. 0.87 Alignments for each domain: == domain 1 score: 309.9 bits; conditional E-value: 1.7e-96 TIGR00657 6 qKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekeliekire 71 +KFGGtSv++ r +++ ++v +++++g v+VVvSA g+TdaL +++ + +++++ e +++i + lcl|FitnessBrowser__Dyella79:N515DRAFT_4002 1 MKFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQEDKGKRVEAARAIAQ 66 7***************************************************************** PP TIGR00657 72 khlealeelasqalkeklkallekeleevkk.......ereldlilsvGEklSaallaaaleelgv 130 +h++ l++++ + ++ ++l e + + + +l+ ++GE +S+al aa l++ g lcl|FitnessBrowser__Dyella79:N515DRAFT_4002 67 RHYDLLDHMQLAVPATLAERLSELAMLAE-DgpgamgeLAWAALVQAHGELMSSALGAAFLSHAG- 130 ********996455555555555555544.3599999778889999*******************. PP TIGR00657 131 kavsllgaeagiltd...sefgrAk.....vleeikterleklleegiivvvaGFiGatekgeitt 188 ++l+a+ + + ++ +r k v + + + + l e g + +++GFi+ + +g++++ lcl|FitnessBrowser__Dyella79:N515DRAFT_4002 131 LPTEWLDARDCLAAValpNQNERTKllsamVEARPDPALNARLAELGEVFITQGFIAREAQGRTVL 196 56666666655444311134444444443244444445555556667******************* PP TIGR00657 189 LGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhp 254 LGRGGSD++A+ +a+lkA++vei+tDV G +ta Pr+vp Ar+l+ ++yeEa+E+as GakvLhp lcl|FitnessBrowser__Dyella79:N515DRAFT_4002 197 LGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQVPGARLLQRLDYEEAQEIASTGAKVLHP 262 ****************************************************************** PP TIGR00657 255 rtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgil 318 r+l p+++ +p+++k+t pe eGT+i+++ e++p vka+s +k +lvs+++++m +g+l lcl|FitnessBrowser__Dyella79:N515DRAFT_4002 263 RCLSPLREPRVPMLIKDTNRPELEGTVIGPEVR-EHAPSVKAISARKGITLVSMESVGMWqqVGFL 327 *******************************77.888*********************9888**** PP TIGR00657 319 aevfgalaeakvnvdlilqsssetsisfvvdked..adkakellkkkvkeekaleevevekklalv 382 a+vf + ++++ +vdli s et+++ +d ++ +d+ + + +++++++v+v a + lcl|FitnessBrowser__Dyella79:N515DRAFT_4002 328 ADVFAQFKQHGLSVDLIG--SAETNVTVSLDPTEnlLDSDAI--AALASDLAKVCRVKVIAPCAAI 389 *****************9..6677877777766633443333..356899**************** PP TIGR00657 383 slvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441 +lvG gm+s ++ ++++ + i ++ is s++ ++++vvde+ ++ ++ lhe l+ lcl|FitnessBrowser__Dyella79:N515DRAFT_4002 390 TLVGRGMRSMLHTLSGVLAEFGQ--IRVHLISqsSNNLNLTFVVDENVVDDLLPHLHELLI 448 *********99999999999999..9999999666778999****************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (853 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 12.56 // [ok]
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