Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_011156172.1 TX73_RS03125 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_000195775.1:WP_011156172.1 Length = 417 Score = 407 bits (1046), Expect = e-118 Identities = 225/416 (54%), Positives = 292/416 (70%), Gaps = 13/416 (3%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQ 60 M +V KFGGTSV +ERI+ VA VK+ D G ++ VVVSAMSG+TN L+ + S Sbjct: 1 MGRLVMKFGGTSVANIERIQNVARHVKREVDAGHEVAVVVSAMSGKTNELVAWCTEASPL 60 Query: 61 PVPRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQR 120 RE D +V++GEQVT LLA+AL G+ A S+ G Q+ ILT AH ARI+ ID Sbjct: 61 HDAREYDAVVASGEQVTSGLLAIALQSLGIQARSWQGWQIPILTSDAHASARIVGIDGSE 120 Query: 121 I-QRDIKAGRVVVVAGFQGVD-EKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGV 178 I +R + V V+AGFQG+ E G ITTLGRGGSDT+ VA+AAALKAD C IYTDVDGV Sbjct: 121 IIKRFSERKEVAVIAGFQGIHAETGRITTLGRGGSDTSAVAIAAALKADRCDIYTDVDGV 180 Query: 179 YTTDPRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSFQE---- 234 YTTDPRVV KA+RLDK++FEEMLE+ASLG+KVLQ+R+VE +++P+ V SF + Sbjct: 181 YTTDPRVVPKARRLDKVSFEEMLELASLGAKVLQVRSVELGMVHNMPIFVRSSFDKPEDI 240 Query: 235 -----GPGTLITLDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANV 289 PGTLI+ EE SME +++GIAF++DEA++++R + D PGVA I GP++ AN+ Sbjct: 241 DPHGTPPGTLIS-SEENSMENHVVTGIAFSKDEAQISVRRIEDKPGVAASIFGPLADANI 299 Query: 290 EVDMIVQNVAHD-NTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGV 348 VDMIVQNV+ D TTD TFTV +D+ A Q + ++G +T++AKVS++G Sbjct: 300 NVDMIVQNVSEDGKTTDLTFTVPASDFARAKQTITSAQDKIGYARFDSETDVAKVSVIGS 359 Query: 349 GMRSHAGVASRMFEALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404 GMRSHAGVA++ F ALA NINI+ I+TSEIK SV+I+ Y ELAVR LHT + LD Sbjct: 360 GMRSHAGVAAQAFAALAARNINIRAITTSEIKFSVLIDAAYTELAVRTLHTLYGLD 415 Lambda K H 0.317 0.133 0.357 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: 423 Number of extensions: 16 Number of successful extensions: 6 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: 417 Length adjustment: 31 Effective length of query: 381 Effective length of database: 386 Effective search space: 147066 Effective search space used: 147066 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_011156172.1 TX73_RS03125 (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.7820.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-128 415.8 6.9 1.1e-128 415.6 6.9 1.0 1 lcl|NCBI__GCF_000195775.1:WP_011156172.1 TX73_RS03125 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195775.1:WP_011156172.1 TX73_RS03125 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 415.6 6.9 1.1e-128 1.1e-128 4 404 .. 4 412 .. 1 415 [. 0.94 Alignments for each domain: == domain 1 score: 415.6 bits; conditional E-value: 1.1e-128 TIGR00656 4 iVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprer 72 V+KFGGtsv+++eri+++a++v++e+ g++v VVvSAms++t+elv+ s re lcl|NCBI__GCF_000195775.1:WP_011156172.1 4 LVMKFGGTSVANIERIQNVARHVKREVDAGHEVAVVVSAMSGKTNELVAWC------TEASPLHDAREY 66 69************************************************9......678888899*** PP TIGR00656 73 delvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvva 141 d +v+ GE+++s ll+ al+ lg +a++ +g++ +ilT+d + +A+i ++ e + e++ + v+a lcl|NCBI__GCF_000195775.1:WP_011156172.1 67 DAVVASGEQVTSGLLAIALQSLGIQARSWQGWQIPILTSDAHASARIVGIDGSEIIKRFSERKEVAVIA 135 ****************************************************666666677789***** PP TIGR00656 142 GFiGat.eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEale 209 GF+G e G+iTtLGRGGSD++A+++aaalkAdr++iyTDV+GvyttDPrvv++a+++dk+s+eE+le lcl|NCBI__GCF_000195775.1:WP_011156172.1 136 GFQGIHaETGRITTLGRGGSDTSAVAIAAALKADRCDIYTDVDGVYTTDPRVVPKARRLDKVSFEEMLE 204 ****76267************************************************************ PP TIGR00656 210 lAtlGakvlhpralelaveakvpilvrsskek........e.egTlitn...kkensslvkaialeknv 266 lA+lGakvl+ r++el + ++pi+vrss++k gTli + ++en+ +v++ia++k+ lcl|NCBI__GCF_000195775.1:WP_011156172.1 205 LASLGAKVLQVRSVELGMVHNMPIFVRSSFDKpedidphgTpPGTLISSeenSMENH-VVTGIAFSKDE 272 *****************************9863333333224699**9877677777.*********** PP TIGR00656 267 arltvegegmlgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesga 331 a+++v+ + +k+g++a if+ La+++invd+i+q se t+++++v d +ak+++++ +++ lcl|NCBI__GCF_000195775.1:WP_011156172.1 273 AQISVR--RIEDKPGVAASIFGPLADANINVDMIVQNVSEdgktTDLTFTVPASDFARAKQTITSAQDK 339 ******..*******************************99999************************* PP TIGR00656 332 aelesleveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrkl 400 +++ + + e d+a+vs++g+g++++ Gva+++f+al+ +nini i++se+k svl+d +++e avr+l lcl|NCBI__GCF_000195775.1:WP_011156172.1 340 IGYARFDSETDVAKVSVIGSGMRSHAGVAAQAFAALAARNINIRAITTSEIKFSVLIDAAYTELAVRTL 408 ********************************************************************* PP TIGR00656 401 hekl 404 h + lcl|NCBI__GCF_000195775.1:WP_011156172.1 409 HTLY 412 *866 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (417 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8.00 // [ok]
This GapMind analysis is from Apr 10 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