Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate 642682810 Cphamn1_0296 homoserine kinase (EC 2.7.1.39)
Query= reanno::Cola:Echvi_2001 (311 letters) >IMG__ChlphaBS1_FD:642682810 Length = 320 Score = 298 bits (763), Expect = 1e-85 Identities = 161/320 (50%), Positives = 209/320 (65%), Gaps = 12/320 (3%) Query: 1 MKKVTAFAPATVANVSCGFDILGFAVEEMGDKVTVSLADEPG----VRVVRIEGDGGRLP 56 MK VT FA AT+ NV+CGFD+LGFA+ E GD+V ++L +E V + I GDGG LP Sbjct: 1 MKTVTGFASATIGNVACGFDVLGFAITEPGDEVILTLREERSGELPVSITSITGDGGALP 60 Query: 57 YEVDKNTCGVALKAFLA------AIDYKGGLEVELYKGLPLGSGMGSSAASSVAALEAAN 110 KNT + FL ID++G +E+EL K LPL SGMGSSAAS+ AAL AAN Sbjct: 61 RNPKKNTSSFVVLKFLEYIRTNKGIDFEGHIELELKKNLPLSSGMGSSAASAAAALVAAN 120 Query: 111 QLLGNPLDKKALLPFAMKAEGVACGAEHADNVAPSLLGGFVLIRSYHPLDVTKLHVPKGL 170 +L+G P +K L+ FA++ E VACG+ HADN AP++LG FVLIRSY+P+D+ + P L Sbjct: 121 ELMGRPCNKMELVNFAIEGERVACGSAHADNAAPAMLGNFVLIRSYNPIDLITIPSPDNL 180 Query: 171 YCALVHPHLELNTADSRSVLRQQVPLKDAITQSGNIAGLVAGLYQEDMGLISRSLQDVIA 230 YC LVHPH+E+ TA +RSVL + + LK A Q GN+ L++GL D LI RSL DVIA Sbjct: 181 YCTLVHPHIEVRTAYARSVLPRMISLKTATEQWGNVGALISGLLTSDYELIGRSLVDVIA 240 Query: 231 EPSRSVLIPGFDEIKSAIKEVGALGVGISGSGPTTFILAPSREVAERASEICQEVFD--K 288 EP R+ LIPGF ++K A E GA+G I+GSGP+ F + S E A R E Q F K Sbjct: 241 EPKRAPLIPGFYDVKHAALEAGAIGCSIAGSGPSIFAFSSSPETASRVGEAMQTAFSTLK 300 Query: 289 IGLEVDLYVSAVNTKGTYVI 308 L+ D+++S V +G VI Sbjct: 301 EKLQSDIWISPVCKQGAKVI 320 Lambda K H 0.317 0.136 0.383 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: 248 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: 311 Length of database: 320 Length adjustment: 27 Effective length of query: 284 Effective length of database: 293 Effective search space: 83212 Effective search space used: 83212 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: 48 (23.1 bits)
Align candidate 642682810 Cphamn1_0296 (homoserine kinase (EC 2.7.1.39))
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.3505976.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-64 201.2 0.0 1e-63 201.0 0.0 1.0 1 IMG__ChlphaBS1_FD:642682810 Domain annotation for each sequence (and alignments): >> IMG__ChlphaBS1_FD:642682810 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 201.0 0.0 1e-63 1e-63 7 284 .. 10 299 .. 5 320 .] 0.86 Alignments for each domain: == domain 1 score: 201.0 bits; conditional E-value: 1e-63 TIGR00191 7 assANlgpGfDvlGlalslvlellvtedvaqeskdk...sleaegegvekipkesdkNliyqvakkvlkklgkr.....vkp 80 a+ N++ GfDvlG a+++ + ++ + s + s+++ + + +p +++kN v++k+l+ + IMG__ChlphaBS1_FD:642682810 10 ATIGNVACGFDVLGFAITEPGDEVILTLREERSG-ElpvSITSITGDGGALPRNPKKNTSSFVVLKFLEYIRTNkgidfEGH 90 7889*************99865555553333333.2468999999999**********777666666654433323335567 PP TIGR00191 81 vkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg......HpDNvapallGGlqlavkeddllev 156 ++l+++k++pl++G+GSSaa+ +aa++aanel+g +++k+el+++a++ E+ H+DN+apa+lG ++l +++ + IMG__ChlphaBS1_FD:642682810 91 IELELKKNLPLSSGMGSSAASAAAALVAANELMGRPCNKMELVNFAIEGERvacgsaHADNAAPAMLGNFVLIRSYNP-IDL 171 99****************************************************************************.999 PP TIGR00191 157 lkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvtAlvskdkadllaiamkDrvhqpyRekliPelt 238 + +Ps ++l++ lv P+iev Ta aR vLP+ s++ + + +++ l+ l + +l+ + D++++p+R+ liP++ IMG__ChlphaBS1_FD:642682810 172 ITIPSPDNLYCTLVHPHIEVRTAYARSVLPRMISLKTATEQWGNVGALISGLLTS-DYELIGRSLVDVIAEPKRAPLIPGFY 252 999999*************************************************.6677777788**************** PP TIGR00191 239 eikqaakekgalgitlSGaGptilalaeeek.eekaqelleklakeg 284 ++k+aa e+ga+g + G+Gp+i+a+++ + + ++ e++++ IMG__ChlphaBS1_FD:642682810 253 DVKHAALEAGAIGCSIAGSGPSIFAFSSSPEtASRVGEAMQTAFSTL 299 ***************************99998888888777655443 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (320 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 19.16 // [ok]
This GapMind analysis is from Jul 25 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