Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_059149707.1 V474_RS00925 homoserine kinase
Query= reanno::Korea:Ga0059261_3253 (319 letters) >NCBI__GCF_001046635.1:WP_059149707.1 Length = 334 Score = 325 bits (833), Expect = 9e-94 Identities = 177/321 (55%), Positives = 215/321 (66%), Gaps = 11/321 (3%) Query: 1 MAVYTQVSAEALAGFLARYDVGELVSAKGIAEGVENSNYLVET-----TRDRFILTLYEK 55 MAVYT++ AE +A ++ +DVG LVSAKGIAEGV NSN+L+ET + RFILT+YE Sbjct: 1 MAVYTRLGAEEMAVIISAFDVGTLVSAKGIAEGVSNSNWLIETQDAAGSARRFILTMYES 60 Query: 56 RVEAADLPYFMGLLDHLAAKGLPVPPAIKDRGGVEI---QELNGRPA-CLIKFLSGISLS 111 R E A+LP+F+ LLDHLAAK PVP + D G Q G A LI+FL G+S+S Sbjct: 61 RTEVAELPFFLDLLDHLAAKHCPVPRTMHDSEGASHRLHQTPEGTKALALIEFLPGVSVS 120 Query: 112 HPTPAQARAAGEAMAQMHRAVADFPLDRPNSMGVDTWQPLFEKCGHS-LDQIVPGLYDDL 170 PTPAQARA G A+AQ+H A ADFP R NS+ + WQ L CG L+ I P L + Sbjct: 121 EPTPAQARAVGGALAQIHLAAADFPASRTNSLALADWQQLLRDCGREGLESIHPELGHIV 180 Query: 171 GFAIARVVPAWTRNDFDRCAIHADLFPDNVLMRGDQVTGLIDFYFACTDIRVYDLAVMHS 230 +A + W R D IHADLFPDNVLM GD VTGLIDFYFACTD+ YD+AV H+ Sbjct: 181 ERELALLAARWPR-DLPSGVIHADLFPDNVLMLGDTVTGLIDFYFACTDLFAYDVAVTHA 239 Query: 231 AWSFDAHGRNYDPAVGDALIAGYEASFPLTEVERAAFPTLAAGACIRFSLSRAWDWLNTP 290 AW F G + PA+ DAL+AGY A PL+ E AA P LA GA +RF +RA+DWLNTP Sbjct: 240 AWCFSPDGTRFLPALSDALMAGYSAVRPLSPAEHAALPLLARGAAMRFLATRAYDWLNTP 299 Query: 291 ADALVMRKDPLAYVRRLKHYA 311 ADALV KDP+A+ RRL+ YA Sbjct: 300 ADALVTPKDPMAFARRLEFYA 320 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: 343 Number of extensions: 15 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: 319 Length of database: 334 Length adjustment: 28 Effective length of query: 291 Effective length of database: 306 Effective search space: 89046 Effective search space used: 89046 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_059149707.1 V474_RS00925 (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.3086301.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-110 355.6 0.0 1.4e-110 355.4 0.0 1.0 1 NCBI__GCF_001046635.1:WP_059149707.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001046635.1:WP_059149707.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 355.4 0.0 1.4e-110 1.4e-110 1 306 [. 1 317 [. 1 318 [. 0.95 Alignments for each domain: == domain 1 score: 355.4 bits; conditional E-value: 1.4e-110 TIGR00938 1 mavytsvsdeeleafLegydlGellslkGiaeGvensnyllttd.....kgryvLtlyekrvkaeeLPfflel 68 mavyt + ee+ ++ +d+G l+s kGiaeGv nsn+l++t+ +r++Lt+ye r++ eLPffl+l NCBI__GCF_001046635.1:WP_059149707.1 1 MAVYTRLGAEEMAVIISAFDVGTLVSAKGIAEGVSNSNWLIETQdaagsARRFILTMYESRTEVAELPFFLDL 73 9******************************************73333358********************** PP TIGR00938 69 lthLaerglpvakpvksrdG...ralseLaGkPa.alvefLkGssvakPtaercrevgevlaklhlagadfke 137 l+hLa++ pv+++++ +G r+ ++ +G a al+efL+G sv++Pt++++r+vg la++hla+adf++ NCBI__GCF_001046635.1:WP_059149707.1 74 LDHLAAKHCPVPRTMHDSEGashRLHQTPEGTKAlALIEFLPGVSVSEPTPAQARAVGGALAQIHLAAADFPA 146 *****************9993333457777855549************************************* PP TIGR00938 138 erkndlrleaWsilaakk.fkvleqleeelaalldkeldalkkflprdLPrgvihadlfkdnvlldgdklkgv 209 +r+n+l l++W+ l + ++ le +++el++ +++el+ l +prdLP+gvihadlf+dnvl+ gd ++g+ NCBI__GCF_001046635.1:WP_059149707.1 147 SRTNSLALADWQQLLRDCgREGLESIHPELGHIVERELALLAARWPRDLPSGVIHADLFPDNVLMLGDTVTGL 219 ******************99***************************************************** PP TIGR00938 210 idfyfaCedallydlaiavndWcfeadd.kldaaaakallkgyeavrpLseeekaafpvllrgaalrfllsrl 281 idfyfaC+d ++yd+a++ +Wcf d+ ++ a al+ gy avrpLs+ e+aa+p l+rgaa+rfl +r+ NCBI__GCF_001046635.1:WP_059149707.1 220 IDFYFACTDLFAYDVAVTHAAWCFSPDGtRFLPALSDALMAGYSAVRPLSPAEHAALPLLARGAAMRFLATRA 292 *************************9962699***************************************** PP TIGR00938 282 ldlvftqagelvvakdPaeferkLk 306 d+ +t+a++lv++kdP +f r+L+ NCBI__GCF_001046635.1:WP_059149707.1 293 YDWLNTPADALVTPKDPMAFARRLE 317 ***********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (334 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: 15.72 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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