Align aspartokinase I (alpha and beta subunits) (EC 2.7.2.4) (characterized)
to candidate WP_010530678.1 ON01_RS08880 aspartate kinase
Query= metacyc::BSU16760-MONOMER (404 letters) >NCBI__GCF_000224785.1:WP_010530678.1 Length = 410 Score = 491 bits (1265), Expect = e-143 Identities = 248/403 (61%), Positives = 314/403 (77%) Query: 1 MKIIVQKFGGTSVKDDKGRKLALGHIKEAISEGYKVVVVVSAMGRKGDPYATDSLLGLLY 60 M+I+VQKFGGTSV+ + R + HIK A+ YK+VVVVSA+GRK PYATDSLL L+ Sbjct: 1 MQILVQKFGGTSVQTEDNRTHVIQHIKNALMNDYKIVVVVSALGRKPAPYATDSLLDLVD 60 Query: 61 GDQSAISPREQDLLLSCGETISSVVFTSMLLDNGVKAAALTGAQAGFLTNDQHTNAKIIE 120 ++ S RE D+L+SCGETI+SVV ++ L N + A ALTGAQAGF+TND AKI E Sbjct: 61 FPKNYNSNRELDILMSCGETIASVVLSNELQKNHISATALTGAQAGFVTNDDFNQAKIKE 120 Query: 121 MKPERLFSVLANHDAVVVAGFQGATEKGDTTTIGRGGSDTSAAALGAAVDAEYIDIFTDV 180 +KP+R+ + HD VVVAGFQG + G+ TTIGRGGSDT+AAA+GAAV+AE I+IFTDV Sbjct: 121 VKPDRVLNEFKEHDVVVVAGFQGQSSDGEITTIGRGGSDTTAAAMGAAVNAERIEIFTDV 180 Query: 181 EGVMTADPRVVENAKPLPVVTYTEICNLAYQGAKVISPRAVEIAMQAKVPIRVRSTYSND 240 G+MTADP VV +A+PL +VTYTEICNLAYQGAKVI PRAVEIAMQAK+P+RVRSTY D Sbjct: 181 NGIMTADPSVVSSARPLDIVTYTEICNLAYQGAKVIHPRAVEIAMQAKIPMRVRSTYVED 240 Query: 241 KGTLVTSHHSSKVGSDVFERLITGIAHVKDVTQFKVPAKIGQYNVQTEVFKAMANAGISV 300 +GTL+T+ ++G+D+ +RLITGIAH+ +TQ V K + +Q++VFKAMA AGISV Sbjct: 241 EGTLITASRIQEMGTDIPDRLITGIAHMSSITQISVQTKEETHRLQSDVFKAMAEAGISV 300 Query: 301 DFFNITPSEIVYTVAGNKTETAQRILMDMGYDPMVTRNCAKVSAVGAGIMGVPGVTSKIV 360 DF NI+P+ ++YTV T+ A IL +G+ P +T+NCAKVSAVGAG+ GVPGV SKIV Sbjct: 301 DFINISPNGVIYTVPDTHTKKAVHILETLGFYPEITKNCAKVSAVGAGMTGVPGVASKIV 360 Query: 361 SALSEKEIPILQSADSHTTIWVLVHEADMVPAVNALHEVFELS 403 +L++ + ILQSADSHTTIWVL+HE D+ PAVNALH+VF L+ Sbjct: 361 QSLTDAGVQILQSADSHTTIWVLIHEDDLKPAVNALHDVFALN 403 Lambda K H 0.316 0.131 0.364 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: 523 Number of extensions: 11 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: 404 Length of database: 410 Length adjustment: 31 Effective length of query: 373 Effective length of database: 379 Effective search space: 141367 Effective search space used: 141367 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_010530678.1 ON01_RS08880 (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.2643585.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-131 422.7 8.9 9.2e-131 422.5 8.9 1.0 1 NCBI__GCF_000224785.1:WP_010530678.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010530678.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 422.5 8.9 9.2e-131 9.2e-131 1 406 [. 1 402 [. 1 403 [. 0.97 Alignments for each domain: == domain 1 score: 422.5 bits; conditional E-value: 9.2e-131 TIGR00656 1 veliVqKFGGtsvgsserikkaakivlkelkegkkvvVVvSAmskvtdelvelaellklleaisdeisprerd 73 +++ VqKFGGtsv+ +++ ++ ++++++l++++k vVVvSA++++ +++ + ll+l++ ++ s+re d NCBI__GCF_000224785.1:WP_010530678.1 1 MQILVQKFGGTSVQTEDNRTHVIQHIKNALMNDYKIVVVVSALGRKPAPYATDS-LLDLVDFPKNYNSNRELD 72 6899**************************************************.9***************** PP TIGR00656 74 elvsvGEllssallssalrelgvkaealdgkeagilTddefgnAkikelateerLlelLeegiivvvaGFiGa 146 l+s+GE+++s++ls+ l+++ a+al+g++ag++T+d f++Akike+++ r+l+ +e+++vvvaGF+G+ NCBI__GCF_000224785.1:WP_010530678.1 73 ILMSCGETIASVVLSNELQKNHISATALTGAQAGFVTNDDFNQAKIKEVKP-DRVLNEFKEHDVVVVAGFQGQ 144 ***************************************************.999999*************** PP TIGR00656 147 teeGeiTtLGRGGSDltAallaaalkAdrveiyTDVeGvyttDPrvveeakkidkisyeEalelAtlGakvlh 219 ++GeiTt+GRGGSD+tAa+++aa++A+r+ei+TDV+G++t+DP vv++a+++d ++y+E+++lA++Gakv+h NCBI__GCF_000224785.1:WP_010530678.1 145 SSDGEITTIGRGGSDTTAAAMGAAVNAERIEIFTDVNGIMTADPSVVSSARPLDIVTYTEICNLAYQGAKVIH 217 ************************************************************************* PP TIGR00656 220 pralelaveakvpilvrsskekeegTlitn....kkens...slvkaialeknvarltvegegmlgkrgilae 285 pra+e+a++ak+p++vrs++ ++egTlit+ ++ ++ +l+++ia+ +++++v+ + + + +++ NCBI__GCF_000224785.1:WP_010530678.1 218 PRAVEIAMQAKIPMRVRSTYVEDEGTLITAsriqEMGTDipdRLITGIAHMSSITQISVQ--TKEETHRLQSD 288 ******************************6665444447799*****************..88888999*** PP TIGR00656 286 ifkaLaeeeinvdlisqtesetsislvvdeedvdeakkaLkeesgaaelesleveedlavvsivgaglveapG 358 +fka+ae++i+vd+i++++ + + ++v ++ +++a+++L++ e+ +++a+vs+vgag++++pG NCBI__GCF_000224785.1:WP_010530678.1 289 VFKAMAEAGISVDFINISP--NGVIYTVPDTHTKKAVHILETLGFYP-----EITKNCAKVSAVGAGMTGVPG 354 *******************..*********************97443.....5889***************** PP TIGR00656 359 vaseifkaleekninilmisssetkisvlvdekdaekavrklheklee 406 vas+i++ l + +++il++++s+t+i+vl++e d++ av++lh+++ + NCBI__GCF_000224785.1:WP_010530678.1 355 VASKIVQSLTDAGVQILQSADSHTTIWVLIHEDDLKPAVNALHDVFAL 402 ********************************************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (407 nodes) Target sequences: 1 (410 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 26.15 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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