Align Homoserine kinase; HK; HSK; EC 2.7.1.39 (characterized)
to candidate RR42_RS15065 RR42_RS15065 serine kinase
Query= SwissProt::P29364 (316 letters) >FitnessBrowser__Cup4G11:RR42_RS15065 Length = 327 Score = 222 bits (566), Expect = 8e-63 Identities = 135/327 (41%), Positives = 183/327 (55%), Gaps = 14/327 (4%) Query: 1 MSVFTPLERSTLEAFLAPYDLGRLRDFRGIAEGSENSNFFVSLEHG----EFVLTLVERG 56 M+VFT + + ++L Y+LG +RD RGIA G ENSNFF+++E E+VLT+ ER Sbjct: 1 MAVFTTVSPDEIASWLLDYNLGEMRDLRGIASGIENSNFFLTMEQDGVTREYVLTIFERL 60 Query: 57 PVQDLPFFIELLDVLHEDGLPVPYALRTRDGEALRRLEGKPALLQPRLAGRHERQPNAHH 116 + LP+++ L+ L + VP + RDGE LR L+GKPA + RL G + P Sbjct: 61 TFEQLPYYLHLMAHLAAHDIRVPAPIPGRDGEILRALKGKPATIVTRLPGGSQLAPGVGQ 120 Query: 117 CQEVGDLLGHLHAATRGRILERPSDRGLPWMLEQGANLAPRLPEQARALLAPALAEIAAL 176 C +VGD+L +H A + ++P+ R LPW + + P L +ALL LA A Sbjct: 121 CAQVGDMLARMHLAGQSYPRQQPNLRSLPWWQQTEGEILPFLDAGQQALLREELAHQTAF 180 Query: 177 --DAERPALPRANLHADLFRDNVLF-DGP----HLAGLIDFYNACSGWMLYDLAITLNDW 229 A+ ALP H DLFRDN LF DGP L G DFY A + L+DLA+T+NDW Sbjct: 181 FGGADYAALPGGPCHCDLFRDNALFEDGPAGQEKLGGFFDFYFAGNDKWLFDLAVTVNDW 240 Query: 230 CSN-TDGSLDPARARALLAAYANRRPFTALEAEHWPSMLRVACVRFWLSRLIAAEAFAGQ 288 C + G+LD R +ALL AY RP +EA HW MLR +RFW+SRL Sbjct: 241 CIDLASGALDADRGQALLRAYHAVRPLGPIEARHWRDMLRAGALRFWISRLWDFYLPREA 300 Query: 289 DVL-IHDPAEFEIRLAQRQNVEIHLPF 314 D+L HDP FE R+ +R+ LP+ Sbjct: 301 DMLQPHDPTHFE-RILRRRIEAAALPW 326 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: 321 Number of extensions: 18 Number of successful extensions: 5 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: 327 Length adjustment: 28 Effective length of query: 288 Effective length of database: 299 Effective search space: 86112 Effective search space used: 86112 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 RR42_RS15065 RR42_RS15065 (serine 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.7243.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-98 314.1 0.0 6e-98 313.9 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS15065 RR42_RS15065 serine kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS15065 RR42_RS15065 serine kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 313.9 0.0 6e-98 6e-98 1 306 [. 1 316 [. 1 317 [. 0.95 Alignments for each domain: == domain 1 score: 313.9 bits; conditional E-value: 6e-98 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttdk....gryvLtlyekrvkaeeLPff 65 mav+t+vs +e+ ++L y+lGe+ +l+Gia+G+ensn++lt ++ + yvLt++e+ + e+LP++ lcl|FitnessBrowser__Cup4G11:RR42_RS15065 1 MAVFTTVSPDEIASWLLDYNLGEMRDLRGIASGIENSNFFLTMEQdgvtREYVLTIFERLT-FEQLPYY 68 9*****************************************985444479*********9.******* PP TIGR00938 66 lellthLaerglpvakpvksrdGralseLaGkPaalvefLkGssvakPtaercrevgevlaklhlagad 134 l+l+ hLa++++ v++p++ rdG+ l L+GkPa++v L+G s P + +c++vg++la++hlag++ lcl|FitnessBrowser__Cup4G11:RR42_RS15065 69 LHLMAHLAAHDIRVPAPIPGRDGEILRALKGKPATIVTRLPGGSQLAPGVGQCAQVGDMLARMHLAGQS 137 ********************************************************************* PP TIGR00938 135 fkeerkndlrleaWsilaakkfkvleqleeelaalldkeldalkkflp....rdLPrgvihadlfkdnv 199 ++ ++ n lr W+ +++ + +l++l+++++all++el++ + f++ LP g h dlf+dn lcl|FitnessBrowser__Cup4G11:RR42_RS15065 138 YPRQQPN-LRSLPWWQQTEGE--ILPFLDAGQQALLREELAHQTAFFGgadyAALPGGPCHCDLFRDNA 203 *******.**********998..*******************999976333367*************** PP TIGR00938 200 lld....g.dklkgvidfyfaCedallydlaiavndWcfe.addkldaaaakallkgyeavrpLseeek 262 l++ g +kl+g+ dfyfa +d +l+dla++vndWc++ a + lda++ +all +y+avrpL ++e lcl|FitnessBrowser__Cup4G11:RR42_RS15065 204 LFEdgpaGqEKLGGFFDFYFAGNDKWLFDLAVTVNDWCIDlASGALDADRGQALLRAYHAVRPLGPIEA 272 **844432246****************************96789************************* PP TIGR00938 263 aafpvllrgaalrfllsrlldlvftqagelvvakdPaeferkLk 306 + +lr++alrf++srl+d++ ++ ++ ++ dP++fer+L+ lcl|FitnessBrowser__Cup4G11:RR42_RS15065 273 RHWRDMLRAGALRFWISRLWDFYLPREADMLQPHDPTHFERILR 316 ******************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (327 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: 10.64 // [ok]
This GapMind analysis is from Apr 09 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