Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_011384021.1 AMB_RS08140 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_000009985.1:WP_011384021.1 Length = 406 Score = 441 bits (1134), Expect = e-128 Identities = 235/407 (57%), Positives = 302/407 (74%), Gaps = 3/407 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MA IV KFGGTSV +ERI+ VA +VK+ +AG+ V VVVSAMSG TN+L+ NQ+ Sbjct: 1 MARIVMKFGGTSVADIERIKNVANRVKREFDAGNQVAVVVSAMSGATNQLVAWCNQVAPL 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 RE D +V+TGEQVT LL++AL + GV A S+ G Q+ I TD H KARI+ I+ Sbjct: 61 HDAREYDAVVATGEQVTTGLLAIALQELGVNARSWCGWQLPIRTDGVHGKARIMSIETDE 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 + A + G V VVAGFQG+ + I TLGRGGSDT+ VALAAAL AD C IYTDVDGVYT Sbjct: 121 MIARMGKGEVAVVAGFQGLGPDNRIATLGRGGSDTSAVALAAALHADRCDIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDPR+V A++LDKIT+EEMLE+AS+G+KVLQ R+VE A K+ V ++VL SF++ PGTL+ Sbjct: 181 TDPRIVSVAKKLDKITYEEMLELASVGAKVLQTRSVEMAMKHRVRVQVLSSFEDKPGTLV 240 Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300 DE+E +E+ ++SGIA++RDEAK+T+ V D PGVA I GP++ A V VDMIVQNV+ Sbjct: 241 C--DEDEIVEKELVSGIAYSRDEAKITLVRVADRPGVAASIFGPLAEAAVNVDMIVQNVS 298 Query: 301 HD-NTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVAS 359 D +TD TFTV D A ++L+ N+G + + D N+ KVS++GVGMRSHAG+A Sbjct: 299 EDGKSTDLTFTVGNADLERAKKVLEDAKGNLGFEKLLADPNVVKVSVIGVGMRSHAGIAQ 358 Query: 360 RMFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELDA 406 +MF+ LA E INIQ+ISTSEIK+SV+IEEKY ELA+RALHTA+ LDA Sbjct: 359 KMFQTLASEGINIQVISTSEIKISVLIEEKYTELALRALHTAYGLDA 405 Lambda K H 0.317 0.133 0.362 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: 437 Number of extensions: 14 Number of successful extensions: 4 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: 412 Length of database: 406 Length adjustment: 31 Effective length of query: 381 Effective length of database: 375 Effective search space: 142875 Effective search space used: 142875 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: 50 (23.9 bits)
Align candidate WP_011384021.1 AMB_RS08140 (aspartate kinase)
to HMM TIGR00656 (aspartate kinase, monofunctional class (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/TIGR00656.hmm # target sequence database: /tmp/gapView.16501.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00656 [M=407] Accession: TIGR00656 Description: asp_kin_monofn: aspartate kinase, monofunctional class 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-135 436.3 10.9 6.8e-135 436.1 10.9 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011384021.1 AMB_RS08140 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011384021.1 AMB_RS08140 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 436.1 10.9 6.8e-135 6.8e-135 3 405 .. 3 402 .. 1 404 [. 0.97 Alignments for each domain: == domain 1 score: 436.1 bits; conditional E-value: 6.8e-135 TIGR00656 3 liVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispre 71 iV+KFGGtsv+++erik++a++v++e g++v VVvSAms+ t++lv+ +++ re lcl|NCBI__GCF_000009985.1:WP_011384021.1 3 RIVMKFGGTSVADIERIKNVANRVKREFDAGNQVAVVVSAMSGATNQLVAWC------NQVAPLHDARE 65 59**************************************************......788888899** PP TIGR00656 72 rdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvv 140 d +v++GE++++ ll+ al+elgv+a++ g++ +i+Td+ +g+A+i +++t +++ ++ +g + vv lcl|NCBI__GCF_000009985.1:WP_011384021.1 66 YDAVVATGEQVTTGLLAIALQELGVNARSWCGWQLPIRTDGVHGKARIMSIET-DEMIARMGKGEVAVV 133 *****************************************************.8999999******** PP TIGR00656 141 aGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEale 209 aGF+G + +i tLGRGGSD++A++laaal+Adr++iyTDV+GvyttDPr+v+ akk+dki+yeE+le lcl|NCBI__GCF_000009985.1:WP_011384021.1 134 AGFQGLGPDNRIATLGRGGSDTSAVALAAALHADRCDIYTDVDGVYTTDPRIVSVAKKLDKITYEEMLE 202 ********************************************************************* PP TIGR00656 210 lAtlGakvlhpralelaveakvpilvrsskekeegTlitn..kkensslvkaialeknvarltvegegm 276 lA++Gakvl+ r++e+a++ v + v ss+e + gTl+++ + +++lv++ia++++ a++t++ + lcl|NCBI__GCF_000009985.1:WP_011384021.1 203 LASVGAKVLQTRSVEMAMKHRVRVQVLSSFEDKPGTLVCDedEIVEKELVSGIAYSRDEAKITLV--RV 269 ****************************************55455669*****************..** PP TIGR00656 277 lgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaeleslevee 341 ++++g++a if+ Lae+ +nvd+i+q se t+++++v + d+++akk+L++ +g++++e+l + lcl|NCBI__GCF_000009985.1:WP_011384021.1 270 ADRPGVAASIFGPLAEAAVNVDMIVQNVSEdgksTDLTFTVGNADLERAKKVLEDAKGNLGFEKLLADP 338 *****************************9999************************************ PP TIGR00656 342 dlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekle 405 ++ +vs++g+g++++ G+a+++f+ l+ ++ini is+se+kisvl++ek++e a r+lh ++ lcl|NCBI__GCF_000009985.1:WP_011384021.1 339 NVVKVSVIGVGMRSHAGIAQKMFQTLASEGINIQVISTSEIKISVLIEEKYTELALRALHTAYG 402 ************************************************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (406 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: 00:00:00.02 # Mc/sec: 6.90 // [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