Align homoserine kinase; EC 2.7.1.39 (characterized)
to candidate 5208569 Shew_1080 homoserine kinase (RefSeq)
Query= CharProtDB::CH_002113 (310 letters) >FitnessBrowser__PV4:5208569 Length = 316 Score = 352 bits (903), Expect = e-102 Identities = 172/304 (56%), Positives = 222/304 (73%), Gaps = 1/304 (0%) Query: 4 VYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAA-ETFSLNNLGRFADKLPSEPRE 62 VYAPAS N+ VGFD+LGAA+ PVDG LLGD V +E+A SL+ G +ADKLP+ E Sbjct: 5 VYAPASMGNVGVGFDLLGAALAPVDGCLLGDRVAIESAPHGVSLSLAGHWADKLPAASEE 64 Query: 63 NIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLNDTR 122 NIVYQC F ++LG + VAMTLEKN+P+GSGLGSSA SVVAAL A+NEH +P + Sbjct: 65 NIVYQCATFFLEQLGSRAGVAMTLEKNLPVGSGLGSSASSVVAALYALNEHFDRPYDSDA 124 Query: 123 LLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGIKV 182 LL LMGE EG+ISGS+HYDNVAPC+LGGMQLM++ + Q +P F +W WV+AYPGI + Sbjct: 125 LLRLMGEFEGKISGSVHYDNVAPCYLGGMQLMLDTPSAVCQGLPVFKDWYWVVAYPGISL 184 Query: 183 STAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAKLMKDVIAEPYRERLLPGF 242 STA+ RA+LPAQY + I GR+L+ F+HA Y + +LA +++KDV+AEPYR +PG+ Sbjct: 185 STAKMRALLPAQYDKSVAIDFGRYLSAFVHASYRQDAKLAIEVLKDVLAEPYRASEIPGY 244 Query: 243 RQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADWLGKNYLQNQEGFVHICRLDT 302 QAR A+ E+G +GISGSGPTLF++ D ETA + WL NY+ + GF HIC++D Sbjct: 245 EQARAALDELGMATTGISGSGPTLFSVTDNLETANKAKAWLDANYVTSGSGFSHICQIDM 304 Query: 303 AGAR 306 G R Sbjct: 305 LGTR 308 Lambda K H 0.321 0.136 0.412 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: 307 Number of extensions: 6 Number of successful extensions: 2 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: 310 Length of database: 316 Length adjustment: 27 Effective length of query: 283 Effective length of database: 289 Effective search space: 81787 Effective search space used: 81787 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate 5208569 Shew_1080 (homoserine kinase (RefSeq))
to HMM TIGR00191 (thrB: homoserine kinase (EC 2.7.1.39))
# 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/TIGR00191.hmm # target sequence database: /tmp/gapView.13698.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00191 [M=304] Accession: TIGR00191 Description: thrB: homoserine kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-90 286.9 0.0 7.8e-90 286.7 0.0 1.0 1 lcl|FitnessBrowser__PV4:5208569 Shew_1080 homoserine kinase (Ref Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5208569 Shew_1080 homoserine kinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 286.7 0.0 7.8e-90 7.8e-90 1 300 [. 3 308 .. 3 312 .. 0.98 Alignments for each domain: == domain 1 score: 286.7 bits; conditional E-value: 7.8e-90 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdk..sleaegegvekipkesdkNliyqvakkvlkklgk 76 l+v++Pas N+g+GfD lG+al +v+++l+++ va+es+ + sl +g+ ++k+p+ s++N++yq+a+ +l++lg lcl|FitnessBrowser__PV4:5208569 3 LTVYAPASMGNVGVGFDLLGAALAPVDGCLLGDRVAIESAPHgvSLSLAGHWADKLPAASEENIVYQCATFFLEQLGS 80 68***********************************9999999********************************** PP TIGR00191 77 rvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg......HpDNvapallGGlqlav 148 r +v++t+ek++p+g+GLGSSa+++vaa++a+ne+++ +++ ll l+++ Eg H+DNvap++lGG+ql++ lcl|FitnessBrowser__PV4:5208569 81 R-AGVAMTLEKNLPVGSGLGSSASSVVAALYALNEHFDRPYDSDALLRLMGEFEGkisgsvHYDNVAPCYLGGMQLML 157 *.**************************************************************************** PP TIGR00191 149 keddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAlvskdkadllaiamkDrvh 226 ++++ +P ++++++v+++P+i++sTa+ Ra+LP++y+ + ++ ++ l+ +v+A + + a+l+ ++kD+++ lcl|FitnessBrowser__PV4:5208569 158 DTPS-AVCQGLPVFKDWYWVVAYPGISLSTAKMRALLPAQYDKSVAIDFGRYLSAFVHASYRQ-DAKLAIEVLKDVLA 233 *999.**********************************************************.89999999****** PP TIGR00191 227 qpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaqelleklakegieltvkvleldtdgae 300 +pyR++ iP++++ + a e g+ ++++SG+Gpt+++++++ + ++ka+ +l+ ++ ++++++++d+ g++ lcl|FitnessBrowser__PV4:5208569 234 EPYRASEIPGYEQARAALDELGMATTGISGSGPTLFSVTDNLEtANKAKAWLDANYVTSGSGFSHICQIDMLGTR 308 ******************************************99**************************99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (316 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: 00:00:00.01 # Mc/sec: 6.35 // [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