Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_092991509.1 BLP65_RS00425 histidinol-phosphate transaminase
Query= metacyc::BSU22620-MONOMER (360 letters) >NCBI__GCF_900102855.1:WP_092991509.1 Length = 368 Score = 263 bits (672), Expect = 5e-75 Identities = 148/356 (41%), Positives = 210/356 (58%), Gaps = 3/356 (0%) Query: 7 LKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQQLALYPDGYS 66 ++ L+PYQPGKPIE ++ E G+ VKLASNENP G S A EA + + LYPDG Sbjct: 12 VRGLQPYQPGKPIEELERELGITNAVKLASNENPLGPSPLAVEAGRKAMTDVGLYPDGNG 71 Query: 67 AALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNAVIEG 126 L+ +L++ + V+ + GNGS +I++ + RAF+ + + F Y A+ Sbjct: 72 FRLKQKLAERIGVAMERITLGNGSSDILEFVVRAFVQPGDTVLFSEHAFAIYPILAMTVS 131 Query: 127 AEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERVPSRVL 186 A+ + R G HDL AM AI +T+VV++ +PNNPTGT+ EL AF+ ++P+ + Sbjct: 132 AKPVSVPAREWG-HDLAAMAAAITPETKVVFVANPNNPTGTWLRGDELEAFIAKMPAETV 190 Query: 187 VVLDEAYYEYVTA--EDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENLIRQ 244 VV+DEAY+EY DYP+ V + KY NL++ RTFSK +GLA LRVGYGI+ + Sbjct: 191 VVVDEAYFEYGRRLESDYPDAVAWVEKYPNLVVSRTFSKCHGLAGLRVGYGISHPGVADL 250 Query: 245 IEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPSQTNF 304 + R PFN + + AAA AALDD A ++ +E N G++Q T GL S NF Sbjct: 251 LNRVRPPFNVNSVALAAAEAALDDDAHLSRTLEVNAEGMKQLAAGFDTLGLSYIGSVGNF 310 Query: 305 VLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEIL 360 + ++ R A +++ALL +G IVR G P LRITIG EQNE +L L +L Sbjct: 311 ISVNVGREAGPVYEALLREGVIVRPIAGYGMPDHLRITIGAAEQNERVLTALNTVL 366 Lambda K H 0.317 0.134 0.382 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: 358 Number of extensions: 13 Number of successful extensions: 3 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: 360 Length of database: 368 Length adjustment: 29 Effective length of query: 331 Effective length of database: 339 Effective search space: 112209 Effective search space used: 112209 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_092991509.1 BLP65_RS00425 (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.17574.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-113 365.5 0.0 1.3e-113 365.4 0.0 1.0 1 lcl|NCBI__GCF_900102855.1:WP_092991509.1 BLP65_RS00425 histidinol-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900102855.1:WP_092991509.1 BLP65_RS00425 histidinol-phosphate transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 365.4 0.0 1.3e-113 1.3e-113 3 348 .. 11 364 .. 9 365 .. 0.98 Alignments for each domain: == domain 1 score: 365.4 bits; conditional E-value: 1.3e-113 TIGR01141 3 kikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkeala 65 ++ l+pYqpg +relg+++ vkL+snEnP+gps+ ++ea +++++++ +Ypd ++++lk++la lcl|NCBI__GCF_900102855.1:WP_092991509.1 11 GVRGLQPYQPGkpieelERELGITNAVKLASNENPLGPSPLAVEAGRKAMTDVGLYPDGNGFRLKQKLA 79 6899***************************************************************** PP TIGR01141 66 kylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedle 134 +++gv +e i+lgnGs +++e+++raf++pgd+vl++e+++++Y++ a++ +a+ ++vp++e+g +dl+ lcl|NCBI__GCF_900102855.1:WP_092991509.1 80 ERIGVAMERITLGNGSSDILEFVVRAFVQPGDTVLFSEHAFAIYPILAMTVSAKPVSVPAREWG-HDLA 147 **************************************************************95.9*** PP TIGR01141 135 avleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee.....asvlella 197 a+++a++ ++k+vf+a+PnnPtG++l +e+e++++++ ++++VVvDeAY e+ ++ ++++ +++ lcl|NCBI__GCF_900102855.1:WP_092991509.1 148 AMAAAITPETKVVFVANPNNPTGTWLRGDELEAFIAKMpAETVVVVDEAYFEYGRRlesdyPDAVAWVE 216 **************************************88**************9999999******** PP TIGR01141 198 eypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveev 266 +ypnlvv+rT+SK +gLAglRvGy+i+++ +++ l++vr+p+nv+s+al+aa aal+d++++++t+e + lcl|NCBI__GCF_900102855.1:WP_092991509.1 217 KYPNLVVSRTFSKCHGLAGLRVGYGISHPGVADLLNRVRPPFNVNSVALAAAEAALDDDAHLSRTLEVN 285 ********************************************************************* PP TIGR01141 267 kkererlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGt 335 ++++++l +++ +l gl+++ S +NF+ ++v ++a ++eall++g+ivR ++ + g+ +++lRit+G lcl|NCBI__GCF_900102855.1:WP_092991509.1 286 AEGMKQLAAGFDTL-GLSYIGSVGNFISVNVGREAGPVYEALLREGVIVRPIAGY-GM-PDHLRITIGA 351 **************.8***************************************.96.********** PP TIGR01141 336 reenerllealke 348 +e+ner+l+al+ lcl|NCBI__GCF_900102855.1:WP_092991509.1 352 AEQNERVLTALNT 364 **********986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (368 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: 00:00:00.01 # Mc/sec: 10.32 // [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