Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_014448869.1 LFE_RS03375 homoserine kinase
Query= BRENDA::Q8L7R2 (370 letters) >NCBI__GCF_000284315.1:WP_014448869.1 Length = 319 Score = 158 bits (399), Expect = 2e-43 Identities = 110/318 (34%), Positives = 171/318 (53%), Gaps = 11/318 (3%) Query: 54 VKTFAPATVANLGPGFDFLGCAVDGLGDHVTLRVDPSVRAGEVSISEITGTTTKLSTNPL 113 V +APA+V N+GPGFD LG AV G+GD +T ++ R+G+ I I+G ++L +P Sbjct: 9 VTVYAPASVGNIGPGFDTLGMAVTGMGDQITGYLEDK-RSGD-RILSISGAWSELPMDPN 66 Query: 114 RNCAGIAAIATMKMLGIRSVGLSLDLHKGLPLGSGLGSSAASAAAAAVAVNEIFGRKLGS 173 +N A IAA + M G+ L + + KG+P GSGLGSSAASA A N + G Sbjct: 67 QNTATIAARTILDMAGLTGKDLVISIEKGVP-GSGLGSSAASAVGGAFLGNILAGNPFSE 125 Query: 174 DQLVLAGLESEAKVS-GYHADNIAPAIMGGF-VLIRNYEPLDLKPLRFPSDKDLFFVLVS 231 +++ A +E++VS GY DN++ + GG V I N + K RF S + + + Sbjct: 126 QEVLEAAANAESRVSGGYFLDNVSACLYGGVTVSITNLK----KSFRFGSLDGVHLLFIV 181 Query: 232 PDFEAPTKKMRAALPTEIPMVHHVWNSSQAAALVAAVLEGDAVMLGKALSSDKIVEPTRA 291 P T + R A+P ++P + V + A ++ AV + + + + +D +V P R Sbjct: 182 PRSLLKTSESRKAIPEKVPFKNSVEAIMRTAGILTAVSSHNQNLFCE-MVNDPLVSPYRG 240 Query: 292 PLIPGMEAVKKAALEAGAFGCTISGAGPTAVAVIDSEEKGQVIGEKMVEAFWKVGHLKSV 351 PLIP A++ A+EAGA ISGAG T VA+ ++ Q + + ++ F +V Sbjct: 241 PLIPLFSAIRDIAVEAGASNLVISGAGSTMVALSPNQTTIQKV-QDTLQPFLDNQEYSAV 299 Query: 352 ASVKKLDNVGARLVNSVS 369 +D+ GAR+VN S Sbjct: 300 LIPSTIDSKGARIVNRTS 317 Lambda K H 0.317 0.133 0.380 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: 250 Number of extensions: 13 Number of successful extensions: 4 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: 370 Length of database: 319 Length adjustment: 29 Effective length of query: 341 Effective length of database: 290 Effective search space: 98890 Effective search space used: 98890 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_014448869.1 LFE_RS03375 (homoserine kinase)
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.14574.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-63 200.0 0.1 2.2e-63 199.9 0.1 1.0 1 lcl|NCBI__GCF_000284315.1:WP_014448869.1 LFE_RS03375 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000284315.1:WP_014448869.1 LFE_RS03375 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 199.9 0.1 2.2e-63 2.2e-63 1 302 [. 9 313 .. 9 315 .. 0.94 Alignments for each domain: == domain 1 score: 199.9 bits; conditional E-value: 2.2e-63 TIGR00191 1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdksleaegegvekipkesdkNliyqvakk 69 ++v++Pas N+gpGfD+lG+a++ + + + + ++ s d + + + +++p ++++N ++ +a lcl|NCBI__GCF_000284315.1:WP_014448869.1 9 VTVYAPASVGNIGPGFDTLGMAVTGMGDQITGYLEDKRSGDR-ILSISGAWSELPMDPNQNTATIAART 76 68************************9999999667777777.66666666****************** PP TIGR00191 70 vlkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg......H 132 +l+ g k + + +ek +p g+GLGSSaa+ v+++ ++n lag+++s++e+l+ a E lcl|NCBI__GCF_000284315.1:WP_014448869.1 77 ILDMAGLTGKDLVISIEKGVP-GSGLGSSAASAVGGAFLGNILAGNPFSEQEVLEAAANAESrvsggyF 144 *********************.9**************************************99****99 PP TIGR00191 133 pDNvapallGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshl 201 DNv+++l GG+++++++ + ++ + s + ++++ ++P ++T e+R+ +P++++ +++v + + lcl|NCBI__GCF_000284315.1:WP_014448869.1 145 LDNVSACLYGGVTVSITNLK--KSFRFGSLDGVHLLFIVPRSLLKTSESRKAIPEKVPFKNSVEAIMRT 211 *****************999..88999999*************************************** PP TIGR00191 202 avlvtAlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek. 269 a++ tA++s+ +++l +++D + pyR liP +++i+ +a e+ga ++++SGaG+t++al+ +++ lcl|NCBI__GCF_000284315.1:WP_014448869.1 212 AGILTAVSSH-NQNLFCEMVNDPLVSPYRGPLIPLFSAIRDIAVEAGASNLVISGAGSTMVALSPNQTt 279 **********.99999*************************************************9998 PP TIGR00191 270 eekaqelleklakegieltvkv.leldtdgaeve 302 +k+q++l+ + ++++ v + ++d +ga+++ lcl|NCBI__GCF_000284315.1:WP_014448869.1 280 IQKVQDTLQPFLDNQEYSAVLIpSTIDSKGARIV 313 99*******9988776666655256788899886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (319 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.44 // [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