Align Aspartate kinase; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_012634396.1 MNOD_RS00510 aspartate kinase
Query= SwissProt::Q88EI9 (411 letters) >NCBI__GCF_000022085.1:WP_012634396.1 Length = 411 Score = 398 bits (1023), Expect = e-115 Identities = 214/410 (52%), Positives = 289/410 (70%), Gaps = 7/410 (1%) Query: 1 MALIVQKFGGTSVGSIERIEQVAEKVKKHREAGDDLVVVLSAMSGETNRLIDLAKQITDQ 60 M +V KFGGTSV +++RI VA V + AG ++ VV+SAM+G+TN L+ K + Sbjct: 1 MPRLVMKFGGTSVATVDRIRNVARHVAREVRAGYEVAVVVSAMAGKTNELVAWCKDASPL 60 Query: 61 PVPRELDVIVSTGEQVTIALLTMALIKRGVPAVSYTGNQVRILTDSSHNKARILQIDDQK 120 E D +V++GEQVT LL + L + G+ A S+ G Q+ I T H ARI +ID + Sbjct: 61 YAQSEYDAVVASGEQVTSGLLAIVLAEMGIKARSWQGWQIPIETSDQHGSARIARIDGSR 120 Query: 121 IRADLKEGRVVVVAGFQGVD-EHGSITTLGRGGSDTTGVALAAALKADECQIYTDVDGVY 179 + A + G V V+AGFQG+ E G +TTLGRGGSDT+ VA+AAA+ A+ C IYTDVDGVY Sbjct: 121 LDAGFRHGEVAVIAGFQGIHAETGRLTTLGRGGSDTSAVAVAAAIGAERCDIYTDVDGVY 180 Query: 180 TTDPRVVPQARRLEKITFEEMLEMASLGSKVLQIRSVEFAGKYNVPLRVLHSFKE----G 235 TTDPRVVP+ARRLE++ FEEMLEMASLG+KVLQ+RSVE A + VP V SF + Sbjct: 181 TTDPRVVPKARRLERVAFEEMLEMASLGAKVLQVRSVELAMVHRVPTTVRSSFDDPDDAR 240 Query: 236 PGTLITIDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISASNIEVDMIV 295 PGTLI DE++ +EQ II+GIAF++DEA++T+R V D PGVA I GP++ +NI VDMI+ Sbjct: 241 PGTLI-CDEDDIVEQQIITGIAFSKDEAQITLRRVKDRPGVAAAIFGPLADANINVDMII 299 Query: 296 QNVAHDN-TTDFTFTVHRNEYEKAQSVLENTAREIGAREVIGDTKIAKVSIVGVGMRSHA 354 Q V+ D TTD TFTV ++YE+A+++L+ + ++ + G T + K+S +GVGMRSHA Sbjct: 300 QVVSGDGVTTDMTFTVPASDYERARTILDAQSGKVEFERIEGATDVVKISAIGVGMRSHA 359 Query: 355 GVASCMFEALAKESINIQMISTSEIKVSVVLEEKYLELAVRALHTAFDLD 404 GVA+ F ALA + INI+ I+TSEIK SV+++ Y ELAVR LH+ + LD Sbjct: 360 GVAAKAFRALADKGINIRAITTSEIKFSVLIDAAYTELAVRTLHSLYGLD 409 Lambda K H 0.316 0.133 0.358 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: 410 Number of extensions: 18 Number of successful extensions: 5 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: 411 Length of database: 411 Length adjustment: 31 Effective length of query: 380 Effective length of database: 380 Effective search space: 144400 Effective search space used: 144400 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_012634396.1 MNOD_RS00510 (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.9673.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-126 406.4 6.6 7.7e-126 406.3 6.6 1.0 1 lcl|NCBI__GCF_000022085.1:WP_012634396.1 MNOD_RS00510 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000022085.1:WP_012634396.1 MNOD_RS00510 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 406.3 6.6 7.7e-126 7.7e-126 4 404 .. 4 406 .. 1 409 [. 0.96 Alignments for each domain: == domain 1 score: 406.3 bits; conditional E-value: 7.7e-126 TIGR00656 4 iVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprer 72 V+KFGGtsv+ ++ri+++a++v +e++ g++v VVvSAm+++t+elv+ + s ++ e lcl|NCBI__GCF_000022085.1:WP_012634396.1 4 LVMKFGGTSVATVDRIRNVARHVAREVRAGYEVAVVVSAMAGKTNELVAWC------KDASPLYAQSEY 66 69*************************************************......8999999***** PP TIGR00656 73 delvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvva 141 d +v+ GE+++s ll+ +l e g ka++ +g++ +i T+d++g+A+i +++ +rL +g + v+a lcl|NCBI__GCF_000022085.1:WP_012634396.1 67 DAVVASGEQVTSGLLAIVLAEMGIKARSWQGWQIPIETSDQHGSARIARIDG-SRLDAGFRHGEVAVIA 134 ****************************************************.**************** PP TIGR00656 142 GFiGat.eeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEale 209 GF+G e G+ TtLGRGGSD++A+++aaa+ A+r++iyTDV+GvyttDPrvv++a++++++++eE+le lcl|NCBI__GCF_000022085.1:WP_012634396.1 135 GFQGIHaETGRLTTLGRGGSDTSAVAVAAAIGAERCDIYTDVDGVYTTDPRVVPKARRLERVAFEEMLE 203 ****76267************************************************************ PP TIGR00656 210 lAtlGakvlhpralelaveakvpilvrsskek....eegTlitn..kkensslvkaialeknvarltve 272 +A+lGakvl+ r++ela+ vp +vrss++ + gTli++ + +++++++ia++k+ a++t++ lcl|NCBI__GCF_000022085.1:WP_012634396.1 204 MASLGAKVLQVRSVELAMVHRVPTTVRSSFDDpddaRPGTLICDedDIVEQQIITGIAFSKDEAQITLR 272 *****************************864222159*****976566668***************** PP TIGR00656 273 gegmlgkrgilaeifkaLaeeeinvdlisqtese....tsislvvdeedvdeakkaLkeesgaaelesl 337 + +++g++a if+ La+++invd+i+q s t+++++v d ++a +L ++sg++e+e++ lcl|NCBI__GCF_000022085.1:WP_012634396.1 273 --RVKDRPGVAAAIFGPLADANINVDMIIQVVSGdgvtTDMTFTVPASDYERARTILDAQSGKVEFERI 339 ..****************************98877889******************************* PP TIGR00656 338 eveedlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklhekl 404 e d+ ++s++g+g++++ Gva+++f al++k+ini i++se+k svl+d +++e avr+lh+ + lcl|NCBI__GCF_000022085.1:WP_012634396.1 340 EGATDVVKISAIGVGMRSHAGVAAKAFRALADKGINIRAITTSEIKFSVLIDAAYTELAVRTLHSLY 406 ****************************************************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (411 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: 00:00:00.01 # Mc/sec: 8.83 // [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