Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (uncharacterized)
to candidate WP_019895100.1 A377_RS0104995 homoserine kinase
Query= curated2:Q9RAM6 (319 letters) >NCBI__GCF_000384235.1:WP_019895100.1 Length = 308 Score = 293 bits (751), Expect = 3e-84 Identities = 144/302 (47%), Positives = 196/302 (64%) Query: 1 MSVFTTVSFEQMQQWLKGYDLGELLDLQGIASGITNTNYFVTTDNGRYVLTLFEEHSAEE 60 MSV+T V+ +Q +L YDLGEL D QGI++GI NTNYFV T GR+VLT+FE+H+ +E Sbjct: 1 MSVYTQVTRTDLQTFLTRYDLGELTDFQGISAGIENTNYFVDTTRGRFVLTIFEQHTLDE 60 Query: 61 LPNFLDLMTHLAERGIPCPHPVKNNAGRALGELNGKPAALVSCLAGRSLDNPMPQHCAAI 120 LP FL++M +AE IP HP+ + GR L L KPAALV L G LDNP P+ C + Sbjct: 61 LPYFLNIMAFMAEHAIPTAHPMADREGRYLQTLKDKPAALVERLQGADLDNPTPRQCEVM 120 Query: 121 GEVLARMHIAGASFKAGMSNLRGQEWRIATAAKVAPFLDEENHRMLDAQLEFERTFDTRR 180 GE LA+ H+AG F +N R W T +++ L E ++ ++ F++ D Sbjct: 121 GEWLAKFHLAGQDFDDFRANDRDLAWAETTYSRLQTKLPAEETALIADEIAFQQQTDWSL 180 Query: 181 LPRGVIHADLFRDNVLMDGDKVGGVIDFYYACHDALLYDIAIAVNDWCVNADCTLDAVRV 240 LP VIHADLF DN L DGD++ G+ID YYAC+ +LYD+A+ +NDWC D TLD+ +V Sbjct: 181 LPVSVIHADLFCDNALFDGDELAGIIDLYYACNGPMLYDLAVMINDWCRRPDQTLDSDKV 240 Query: 241 RAFLDAYHAIRPLTGEEHAAWPGMLRVAAMRFWLSRLNDLYFPQAGELTHAKDPAYFERI 300 L AY +RPL+ EH+AW + R+ A+RF+LSRL D Y P+ GE+T KDP F ++ Sbjct: 241 VRTLQAYETVRPLSEAEHSAWLSVQRMGALRFYLSRLQDQYQPREGEMTQIKDPQVFGKL 300 Query: 301 LK 302 L+ Sbjct: 301 LQ 302 Lambda K H 0.324 0.137 0.430 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: 293 Number of extensions: 6 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: 319 Length of database: 308 Length adjustment: 27 Effective length of query: 292 Effective length of database: 281 Effective search space: 82052 Effective search space used: 82052 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 48 (23.1 bits)
Align candidate WP_019895100.1 A377_RS0104995 (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.3391.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-111 358.0 0.1 2.5e-111 357.8 0.1 1.0 1 lcl|NCBI__GCF_000384235.1:WP_019895100.1 A377_RS0104995 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384235.1:WP_019895100.1 A377_RS0104995 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 357.8 0.1 2.5e-111 2.5e-111 1 306 [. 1 302 [. 1 303 [. 0.98 Alignments for each domain: == domain 1 score: 357.8 bits; conditional E-value: 2.5e-111 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 m+vyt+v+ +l++fL ydlGel +++Gi+ G+en+ny+++t++gr+vLt++e+++ +eLP+fl+++ lcl|NCBI__GCF_000384235.1:WP_019895100.1 1 MSVYTQVTRTDLQTFLTRYDLGELTDFQGISAGIENTNYFVDTTRGRFVLTIFEQHT-LDELPYFLNIM 68 9********************************************************.9********** PP TIGR00938 70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138 ++ae+ +p+a+p++ r+Gr l++L+ kPaalve L+G ++++Pt+++c +ge lak+hlag+df+ lcl|NCBI__GCF_000384235.1:WP_019895100.1 69 AFMAEHAIPTAHPMADREGRYLQTLKDKPAALVERLQGADLDNPTPRQCEVMGEWLAKFHLAGQDFDDF 137 ********************************************************************* PP TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdklk 207 r+n r aW ++ + + +l +e++al+ +e+++ ++ + LP +vihadlf dn l+dgd+l+ lcl|NCBI__GCF_000384235.1:WP_019895100.1 138 RAN-DRDLAWAETTYSR--LQTKLPAEETALIADEIAFQQQTDWSLLPVSVIHADLFCDNALFDGDELA 203 ***.5667899999999..999*********************************************** PP TIGR00938 208 gvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalrf 276 g+id+y+aC++ +lydla+ +ndWc+ d++ld +++ l++ye+vrpLse e+ a+ ++r +alrf lcl|NCBI__GCF_000384235.1:WP_019895100.1 204 GIIDLYYACNGPMLYDLAVMINDWCRRPDQTLDSDKVVRTLQAYETVRPLSEAEHSAWLSVQRMGALRF 272 ********************************************************************* PP TIGR00938 277 llsrlldlvftqagelvvakdPaeferkLk 306 +lsrl+d ++++ ge++++kdP+ f ++L+ lcl|NCBI__GCF_000384235.1:WP_019895100.1 273 YLSRLQDQYQPREGEMTQIKDPQVFGKLLQ 302 **************************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (308 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: 10.58 // [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