Align Histidinol-phosphate aminotransferase; EC 2.6.1.9 (characterized, see rationale)
to candidate WP_013835034.1 THICY_RS02435 histidinol-phosphate transaminase
Query= uniprot:A0A2R7PAQ8 (373 letters) >NCBI__GCF_000214825.1:WP_013835034.1 Length = 369 Score = 271 bits (692), Expect = 3e-77 Identities = 152/363 (41%), Positives = 226/363 (62%), Gaps = 16/363 (4%) Query: 15 IRPDVRAMHSYVVQPSTGMLKMDAMENPFRLPAHLQAALGQRLGSVALNRYPGDRIADLK 74 +R +VRA+++Y V PST M+K+DAMENP+ P L+ A +L ++LNRYP +L Sbjct: 16 VRTEVRAINAYHVPPSTNMIKLDAMENPYGWPDDLRQAWLAKLAELSLNRYPDPSATELH 75 Query: 75 AALAQYAGMPEGYGIVLGNGSDELITLLALACAQPGTGQRATMLAPMPGFVMYPLSAQLQ 134 L ++ + G++ GNGSDE+I LL +A +P A +++ P FVMY + A+ Sbjct: 76 QTLHRHLNLTSATGLLFGNGSDEIIQLLIMAVNKPD----AKVMSIAPTFVMYDMIARFL 131 Query: 135 GLDFVGVPLTPDFELDEPAMLAAIGQHRPAITYIAYPNNPTATLWDEGAVQRIIDAAGAQ 194 G D+ VPL F+LD + + A+ + +PA+ +IAYPNNPT V RII+AA Sbjct: 132 GADYCSVPLDESFQLDVDSFITAMIEQQPALVFIAYPNNPTGNALSRQDVIRIIEAAP-- 189 Query: 195 GGIVVMDEAYQPFASRTWIDRMRAEPARNAHVLLMRTLSKFGLAGVRLGYLIGPSAFVSE 254 G+VV+DEAY FA +++ A P +VL+MRT SK GLAG+RLGYL+GP A++ + Sbjct: 190 -GLVVVDEAYHAFAEDSFVQDTCAYP----NVLVMRTFSKVGLAGLRLGYLVGPVAWIEQ 244 Query: 255 IDKVRPPYNVSVLNCEAALFALEHAEVFAAQAAEIRVERATLIAALRQMPGVEKCWDSEA 314 IDK+R PYN++ + +AL AL H + A QA +I +RA L L ++PGV + S A Sbjct: 245 IDKLRLPYNINTMTQASALVALAHWPILAEQALQICQDRAELAKQLAELPGV-AVYPSAA 303 Query: 315 NMVLIRV----ADSAKAYEGMKNRKVLVKNVSTMHPLLANCLRLTVGNAEDNAQMLAALQ 370 N ++IR+ + +EG+K +L+KN+S +LANCLR+TVG+ +N+Q+L L Sbjct: 304 NFIVIRLDLAGPTATDVFEGLKAVGILIKNLSGQGGVLANCLRITVGSISENSQLLKGLA 363 Query: 371 ASL 373 A L Sbjct: 364 ALL 366 Lambda K H 0.321 0.134 0.392 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: 352 Number of extensions: 19 Number of successful extensions: 6 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: 373 Length of database: 369 Length adjustment: 30 Effective length of query: 343 Effective length of database: 339 Effective search space: 116277 Effective search space used: 116277 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 bits)
Align candidate WP_013835034.1 THICY_RS02435 (histidinol-phosphate transaminase)
to HMM TIGR01141 (hisC: histidinol-phosphate transaminase (EC 2.6.1.9))
# 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/TIGR01141.hmm # target sequence database: /tmp/gapView.14617.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01141 [M=349] Accession: TIGR01141 Description: hisC: histidinol-phosphate transaminase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-103 331.0 0.0 4.3e-103 330.8 0.0 1.0 1 lcl|NCBI__GCF_000214825.1:WP_013835034.1 THICY_RS02435 histidinol-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214825.1:WP_013835034.1 THICY_RS02435 histidinol-phosphate transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 330.8 0.0 4.3e-103 4.3e-103 1 347 [. 17 363 .. 17 365 .. 0.97 Alignments for each domain: == domain 1 score: 330.8 bits; conditional E-value: 4.3e-103 TIGR01141 1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk..klhrYpdpqalelkealaky 67 r +++++++Y+ + + ++++kL+++EnP+g ++ +++a+ ++l+ +l+rYpdp+a+el ++l ++ lcl|NCBI__GCF_000214825.1:WP_013835034.1 17 RTEVRAINAYHVP----PSTNMIKLDAMENPYGWPDDLRQAWLAKLAelSLNRYPDPSATELHQTLHRH 81 6789999999995....66789*************************9999****************** PP TIGR01141 68 lg.veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedlea 135 l+ +++ +l+gnGsde+i+lli+a+ +p ++v+ + pt+ mY ++a++ ga++ +vpl+e++q d+++ lcl|NCBI__GCF_000214825.1:WP_013835034.1 82 LNlTSATGLLFGNGSDEIIQLLIMAVNKPDAKVMSIAPTFVMYDMIARFLGADYCSVPLDESFQLDVDS 150 **556788************************************************************* PP TIGR01141 136 vle.aakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlv 203 + + +++++ lvf+a+PnnPtGn l+r+++++++e++ +lVVvDeAY F+e+ s+++ ypn++ lcl|NCBI__GCF_000214825.1:WP_013835034.1 151 FITaMIEQQPALVFIAYPNNPTGNALSRQDVIRIIEAA-PGLVVVDEAYHAFAED-SFVQDTCAYPNVL 217 9987899******************************8.9**************8.************* PP TIGR01141 204 vlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkerer 272 v+rT+SK+ LAglR+Gy+++ ++ie+++k+r pyn+++++++ a+ al ++ ++++ ++ ++r+ lcl|NCBI__GCF_000214825.1:WP_013835034.1 218 VMRTFSKVG-LAGLRLGYLVGPVAWIEQIDKLRLPYNINTMTQASALVALAHWPILAEQALQICQDRAE 285 *******97.*********************************************************** PP TIGR01141 273 lleelkkleglevyeSkaNFvlikvke...daeelleallekgiivRdlksaeglleeclRitvGtree 338 l ++l++l+g+ vy+S aNF++i+++ +a++++e l+ gi++++l+ + g+l +clRitvG+ +e lcl|NCBI__GCF_000214825.1:WP_013835034.1 286 LAKQLAELPGVAVYPSAANFIVIRLDLagpTATDVFEGLKAVGILIKNLSGQGGVLANCLRITVGSISE 354 *************************988999************************************** PP TIGR01141 339 nerllealk 347 n +ll+ l+ lcl|NCBI__GCF_000214825.1:WP_013835034.1 355 NSQLLKGLA 363 *****9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (369 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.95 // [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