Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate WP_027456813.1 K420_RS0103375 homoserine kinase
Query= SwissProt::P29364 (316 letters) >NCBI__GCF_000519045.1:WP_027456813.1 Length = 308 Score = 204 bits (520), Expect = 2e-57 Identities = 135/316 (42%), Positives = 166/316 (52%), Gaps = 12/316 (3%) Query: 1 MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHGEFVLTLVERGPVQD 60 MSV+TP+ R L A+L P LG L D GIA G +NSN+FV+ G FVLTL E Sbjct: 1 MSVYTPVGRDALAAWLQPLRLGELIDHAGIAAGMQNSNYFVTTAAGRFVLTLFENIDPAA 60 Query: 61 LPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHHCQEV 120 L F++ L D L GLP P L G R L GKPA L L G QP+ HH + + Sbjct: 61 LDFYLALQDRLARAGLPCPQPLTDAAGRRWRPLAGKPAALLTCLPGAALEQPDMHHLRTL 120 Query: 121 GDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAALDAER 180 GD+L LH A G P+ G W G L P + R LLA LA AA D Sbjct: 121 GDMLARLHLAAAGMPDPLPNPCGSAWRQRVGQALLPLVDATERELLADELAFQAAQDWS- 179 Query: 181 PALPRANLHADLFRDNVLF--DGPHLAGLIDFYNACSGWMLYDLAITLNDWCSNTDGSLD 238 ALP +HADLFRDNVL+ DG L+GL+DFY A L+DLA+ NDWC++ G Sbjct: 180 -ALPCGVIHADLFRDNVLWLADG-RLSGLLDFYFAGEDAWLFDLAVVANDWCADERG--- 234 Query: 239 PARARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRL-IAAEAFAGQDVLIHDPAE 297 ALLA Y RP E + WP++ R A +RFWL RL + + G+ V I +P E Sbjct: 235 ---LAALLAGYGAVRPLLPAERQAWPAVRRAAALRFWLLRLEVRHQPRLGEVVTIKNPDE 291 Query: 298 FEIRLAQRQNVEIHLP 313 F LA + LP Sbjct: 292 FRRLLAALRLAGSELP 307 Lambda K H 0.324 0.140 0.434 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: 281 Number of extensions: 12 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: 316 Length of database: 308 Length adjustment: 27 Effective length of query: 289 Effective length of database: 281 Effective search space: 81209 Effective search space used: 81209 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: 41 (22.0 bits) S2: 48 (23.1 bits)
Align candidate WP_027456813.1 K420_RS0103375 (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.28270.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-89 283.8 0.0 9.9e-89 283.6 0.0 1.0 1 lcl|NCBI__GCF_000519045.1:WP_027456813.1 K420_RS0103375 homoserine kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027456813.1 K420_RS0103375 homoserine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 283.6 0.0 9.9e-89 9.9e-89 1 306 [. 1 297 [. 1 298 [. 0.98 Alignments for each domain: == domain 1 score: 283.6 bits; conditional E-value: 9.9e-89 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdkgryvLtlyekrvkaeeLPfflell 69 m+vyt v + l a+L+ lGel++ Gia G++nsny++tt gr+vLtl+e+ + L f+l+l+ lcl|NCBI__GCF_000519045.1:WP_027456813.1 1 MSVYTPVGRDALAAWLQPLRLGELIDHAGIAAGMQNSNYFVTTAAGRFVLTLFENID-PAALDFYLALQ 68 9*****************************************************998.99********* PP TIGR00938 70 thLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagadfkee 138 + La glp+++p++ +Gr LaGkPaal+ +L+G +++P +++ r+ g++la+lhla+a+ + lcl|NCBI__GCF_000519045.1:WP_027456813.1 69 DRLARAGLPCPQPLTDAAGRRWRPLAGKPAALLTCLPGAALEQPDMHHLRTLGDMLARLHLAAAGMPDP 137 ********************************************************************* PP TIGR00938 139 rkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdk.l 206 n + aW+ + + +l+ +++ + +ll +el++ + LP gvihadlf+dnvl +d+ l lcl|NCBI__GCF_000519045.1:WP_027456813.1 138 LPN-PCGSAWRQRVGQA--LLPLVDATERELLADELAFQAAQDWSALPCGVIHADLFRDNVLWLADGrL 203 ***.99********999..*******************************************888777* PP TIGR00938 207 kgvidfyfaCedallydlaiavndWcfeaddkldaaaakallkgyeavrpLseeekaafpvllrgaalr 275 +g++dfyfa eda+l+dla+ ndWc ++ all gy avrpL + e++a+p + r+aalr lcl|NCBI__GCF_000519045.1:WP_027456813.1 204 SGLLDFYFAGEDAWLFDLAVVANDWCADER------GLAALLAGYGAVRPLLPAERQAWPAVRRAAALR 266 **************************8754......4579***************************** PP TIGR00938 276 fllsrlldlvftqagelvvakdPaeferkLk 306 f+l rl ++++ ge+v++k+P ef+r+L+ lcl|NCBI__GCF_000519045.1:WP_027456813.1 267 FWLLRLEVRHQPRLGEVVTIKNPDEFRRLLA 297 ****************************996 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.54 // [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