Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_011444745.1 SARO_RS05420 homoserine kinase
Query= reanno::Korea:Ga0059261_3253 (319 letters) >NCBI__GCF_000013325.1:WP_011444745.1 Length = 328 Score = 355 bits (912), Expect = e-103 Identities = 187/317 (58%), Positives = 224/317 (70%), Gaps = 7/317 (2%) Query: 1 MAVYTQVSAEALAGFLARYDVGELVSAKGIAEGVENSNYLVETT-RD----RFILTLYEK 55 MAVYTQ+ AE +A +A +DVGELVSAKGIAEGV NSN+L++TT RD RFILT+YE Sbjct: 1 MAVYTQIGAEDMAALVAEFDVGELVSAKGIAEGVSNSNWLLDTTGRDGKGARFILTMYEF 60 Query: 56 RVEAADLPYFMGLLDHLAAKGLPVPPAIKDRGGVEIQELNGRPACLIKFLSGISLSHPTP 115 R+E DLPYF+ LLDHLA +G VP I DR G + + LI+FL G+S+S PTP Sbjct: 61 RIELEDLPYFLSLLDHLAGRGCAVPRTIHDRAGALYRMRGDKALALIEFLPGVSVSEPTP 120 Query: 116 AQARAAGEAMAQMHRAVADFPLDRPNSMGVDTWQPLFEKCG-HSLDQIVPGLYDDLGFAI 174 AQARA G A+AQMH A ADF R N MG+ WQ LF+ CG L +I P L + + Sbjct: 121 AQARAVGTALAQMHLASADFAGSRENGMGLAEWQRLFDACGAEGLARIDPDLAGLVAEHM 180 Query: 175 ARVVPAWTRNDFDRCAIHADLFPDNVLMRGDQVTGLIDFYFACTDIRVYDLAVMHSAWSF 234 R+ W D R IHADLFPDNVLM GD+VTGLIDFYFAC DI YD+AV H+AW F Sbjct: 181 PRIAAQWPA-DLPRSVIHADLFPDNVLMLGDKVTGLIDFYFACNDIMAYDVAVTHAAWCF 239 Query: 235 DAHGRNYDPAVGDALIAGYEASFPLTEVERAAFPTLAAGACIRFSLSRAWDWLNTPADAL 294 D GR++DPAV AL+ GYE+ PL ERAA P LA GA +RF+ SRA+DWLNTPADAL Sbjct: 240 DGSGRSFDPAVSAALLEGYESVRPLLPEERAALPLLAQGAAMRFTSSRAYDWLNTPADAL 299 Query: 295 VMRKDPLAYVRRLKHYA 311 V+RKDP+A+ RRL+ YA Sbjct: 300 VVRKDPMAFARRLQFYA 316 Lambda K H 0.323 0.138 0.429 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: 342 Number of extensions: 14 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: 319 Length of database: 328 Length adjustment: 28 Effective length of query: 291 Effective length of database: 300 Effective search space: 87300 Effective search space used: 87300 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 48 (23.1 bits)
Align candidate WP_011444745.1 SARO_RS05420 (homoserine kinase)
to HMM TIGR00938 (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/TIGR00938.hmm # target sequence database: /tmp/gapView.30584.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00938 [M=307] Accession: TIGR00938 Description: thrB_alt: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-109 350.8 0.0 3.9e-109 350.6 0.0 1.0 1 lcl|NCBI__GCF_000013325.1:WP_011444745.1 SARO_RS05420 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013325.1:WP_011444745.1 SARO_RS05420 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 350.6 0.0 3.9e-109 3.9e-109 1 306 [. 1 313 [. 1 314 [. 0.97 Alignments for each domain: == domain 1 score: 350.6 bits; conditional E-value: 3.9e-109 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkg.....ryvLtlyekrvkaeeLPf 64 mavyt++ e++ a + +d+Gel+s kGiaeGv nsn+ll+t+ + r++Lt+ye r + e+LP+ lcl|NCBI__GCF_000013325.1:WP_011444745.1 1 MAVYTQIGAEDMAALVAEFDVGELVSAKGIAEGVSNSNWLLDTTGRdgkgaRFILTMYEFRIELEDLPY 69 9*****************************************9854344459***************** PP TIGR00938 65 flellthLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlaga 133 fl ll+hLa rg +v+++++ r+G++ k al+efL+G sv++Pt++++r+vg la++hla+a lcl|NCBI__GCF_000013325.1:WP_011444745.1 70 FLSLLDHLAGRGCAVPRTIHDRAGALYRMRGDKALALIEFLPGVSVSEPTPAQARAVGTALAQMHLASA 138 ************************99988888999********************************** PP TIGR00938 134 dfkeerkndlrleaWsilaakk.fkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvll 201 df ++r+n ++l++W+ l+ ++ + l ++++la l+ +++ + +p dLPr+vihadlf+dnvl+ lcl|NCBI__GCF_000013325.1:WP_011444745.1 139 DFAGSRENGMGLAEWQRLFDACgAEGLARIDPDLAGLVAEHMPRIAAQWPADLPRSVIHADLFPDNVLM 207 **********************999******************************************** PP TIGR00938 202 dgdklkgvidfyfaCedallydlaiavndWcfead.dkldaaaakallkgyeavrpLseeekaafpvll 269 gdk++g+idfyfaC+d ++yd+a++ +Wcf+ ++d a all+gye+vrpL +ee+aa+p l+ lcl|NCBI__GCF_000013325.1:WP_011444745.1 208 LGDKVTGLIDFYFACNDIMAYDVAVTHAAWCFDGSgRSFDPAVSAALLEGYESVRPLLPEERAALPLLA 276 ********************************976268******************************* PP TIGR00938 270 rgaalrfllsrlldlvftqagelvvakdPaeferkLk 306 +gaa+rf sr+ d+ +t+a++lvv kdP +f r+L+ lcl|NCBI__GCF_000013325.1:WP_011444745.1 277 QGAAMRFTSSRAYDWLNTPADALVVRKDPMAFARRLQ 313 ***********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (328 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: 9.02 // [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