Align Aspartate kinase Ask_LysC; Aspartokinase; EC 2.7.2.4 (characterized)
to candidate WP_013135532.1 ARNIT_RS08635 aspartate kinase
Query= SwissProt::A4VJB4 (412 letters) >NCBI__GCF_000092245.1:WP_013135532.1 Length = 402 Score = 419 bits (1076), Expect = e-121 Identities = 224/403 (55%), Positives = 295/403 (73%), Gaps = 4/403 (0%) Query: 3 LIVQKFGGTSVGTVERIEQVAEKVKKFRDGGDDIVVVVSAMSGETNRLIDLAKQISEQPV 62 L V KFGGTSVGT+ERI+ VA +KK +D G D++ VVSAMSGETN+LI+ A+ S+ P Sbjct: 2 LKVLKFGGTSVGTLERIQNVATIIKKIKDDGHDVIAVVSAMSGETNKLIEYAESYSKMPA 61 Query: 63 PRELDVMVSTGEQVTIALLAMALIKRGVPAVSYTGNQVRILTDSAHTKARILQIDAQRIQ 122 P E+D+++S+GE+VT ALL++AL + G A+S +G + I+TD HTKARI ID + ++ Sbjct: 62 PSEMDMLLSSGERVTSALLSIALNEAGYSAISMSGGRAGIVTDERHTKARIEYIDTKNMK 121 Query: 123 RDIKAGRVVVVAGFQGVDEKGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYTTD 182 I G+VVVVAGFQGV +KG +TTLGRGGSD T VA+A A++AD C+IYTDVDG+YTTD Sbjct: 122 ESIAEGKVVVVAGFQGVTQKGRVTTLGRGGSDLTAVAIAGAIEADVCEIYTDVDGIYTTD 181 Query: 183 PRVVAKAQRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYSVPLRVLHSF-QEGPGTLIT 241 PR+ KA++LDKI+++EMLE+ASLG+KVLQ R+VE A K +V L SF E GTLIT Sbjct: 182 PRIEPKAKKLDKISYDEMLELASLGAKVLQNRSVEMAKKLNVNLISRSSFTPEVEGTLIT 241 Query: 242 LDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVAHD 301 EE MEQPI+SGIA ++++ ++ + GV D PG+A I ++ AN+ VDMIVQ VA D Sbjct: 242 -KEENIMEQPIVSGIALDKNQVRVGMYGVTDRPGIASYIFTALADANINVDMIVQTVAVD 300 Query: 302 NTTDFTFTVHRNDYNNALQVLQGIAAEMGAREAIGDTNIAKVSIVGVGMRSHAGVASRMF 361 T FT+ D ++ E+ + + I KVSIVGVGM+SH GVAS+ F Sbjct: 301 GKTSLDFTIPTTDLEICKTIMHKFEDEVEKFDY--NEKICKVSIVGVGMKSHTGVASKAF 358 Query: 362 EALAKENINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD 404 ALA ENINI++ISTSEIK+SV++EEKY ELAVRALH A++LD Sbjct: 359 TALANENINIRIISTSEIKISVIVEEKYAELAVRALHDAYDLD 401 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: 462 Number of extensions: 11 Number of successful extensions: 3 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: 402 Length adjustment: 31 Effective length of query: 381 Effective length of database: 371 Effective search space: 141351 Effective search space used: 141351 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_013135532.1 ARNIT_RS08635 (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.15683.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-143 463.9 14.7 2.7e-143 463.8 14.7 1.0 1 lcl|NCBI__GCF_000092245.1:WP_013135532.1 ARNIT_RS08635 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092245.1:WP_013135532.1 ARNIT_RS08635 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 463.8 14.7 2.7e-143 2.7e-143 3 406 .. 2 400 .. 1 401 [. 0.97 Alignments for each domain: == domain 1 score: 463.8 bits; conditional E-value: 2.7e-143 TIGR00656 3 liVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeispre 71 l V KFGGtsvg eri+++a i++k + +g++v+ VvSAms++t++l+e a e+ s+ ++p e lcl|NCBI__GCF_000092245.1:WP_013135532.1 2 LKVLKFGGTSVGTLERIQNVATIIKKIKDDGHDVIAVVSAMSGETNKLIEYA------ESYSKMPAPSE 64 6799************************************************......7********** PP TIGR00656 72 rdelvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvv 140 +d+l+s GE+++salls al+e g+ a++++g++agi+Td+++++A+i++++t +++ e ++eg++vvv lcl|NCBI__GCF_000092245.1:WP_013135532.1 65 MDMLLSSGERVTSALLSIALNEAGYSAISMSGGRAGIVTDERHTKARIEYIDT-KNMKESIAEGKVVVV 132 *****************************************************.9************** PP TIGR00656 141 aGFiGateeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEale 209 aGF+G t++G++TtLGRGGSDltA+++a a++Ad +eiyTDV+G+yttDPr+ ++akk+dkisy+E+le lcl|NCBI__GCF_000092245.1:WP_013135532.1 133 AGFQGVTQKGRVTTLGRGGSDLTAVAIAGAIEADVCEIYTDVDGIYTTDPRIEPKAKKLDKISYDEMLE 201 ********************************************************************* PP TIGR00656 210 lAtlGakvlhpralelaveakvpilvrsskeke.egTlitn...kkensslvkaialeknvarltvege 274 lA+lGakvl++r++e+a++ +v+++ rss+ +e egTlit+ +e++ +v++ial+kn+ r+ ++ lcl|NCBI__GCF_000092245.1:WP_013135532.1 202 LASLGAKVLQNRSVEMAKKLNVNLISRSSFTPEvEGTLITKeenIMEQP-IVSGIALDKNQVRVGMY-- 267 ****************************************976567777.*****************.. PP TIGR00656 275 gmlgkrgilaeifkaLaeeeinvdlisqtese...tsislvvdeedvdeakkaLkeesgaaelesleve 340 g+++++gi++ if+aLa+++invd+i+qt + ts+++++ ++d++ k +++++ +e+e+ +++ lcl|NCBI__GCF_000092245.1:WP_013135532.1 268 GVTDRPGIASYIFTALADANINVDMIVQTVAVdgkTSLDFTIPTTDLEICKTIMHKFE--DEVEKFDYN 334 9****************************875666********************996..6777***** PP TIGR00656 341 edlavvsivgaglveapGvaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 e++++vsivg+g+++++Gvas++f+al+++nini is+se+kisv+v+ek+ae avr+lh+++ + lcl|NCBI__GCF_000092245.1:WP_013135532.1 335 EKICKVSIVGVGMKSHTGVASKAFTALANENINIRIISTSEIKISVIVEEKYAELAVRALHDAYDL 400 **************************************************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (402 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 6.83 // [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