Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate PfGW456L13_2177 Biosynthetic Aromatic amino acid aminotransferase beta (EC 2.6.1.57)
Query= metacyc::BSU22620-MONOMER (360 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 Length = 370 Score = 272 bits (696), Expect = 9e-78 Identities = 150/356 (42%), Positives = 209/356 (58%), Gaps = 3/356 (0%) Query: 7 LKQLKPYQPGKPIEAVKSEYGLD--KVVKLASNENPYGCSEAAKEALHHEIQQLALYPDG 64 ++QL PY PGKP++ + E LD ++KLASNENP G A A+ + +L YPDG Sbjct: 13 VQQLSPYVPGKPVDELARELDLDPASIIKLASNENPLGAGPKALAAIRDALAELTRYPDG 72 Query: 65 YSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNAVI 124 AL++ L++ V + GNGS++I++++ RA+L N V + F Y Sbjct: 73 NGFALKSLLAEQCRVELDQVTLGNGSNDILELVARAYLAPGLNAVFSEHAFAVYPIATQA 132 Query: 125 EGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERVPSR 184 GA+ + + + D HDL AML AID T+VV+I +PNNPTGT+ L FL+ VP Sbjct: 133 VGAQAKVVPAK-DWGHDLPAMLAAIDANTRVVFIANPNNPTGTWFDAEALDEFLQDVPEH 191 Query: 185 VLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENLIRQ 244 VLVVLDEAY EY D P+ + L+ Y NL++ RTFSKAYGLAALRVGYG++ + Sbjct: 192 VLVVLDEAYIEYAEGSDLPDGLDFLAAYPNLLVSRTFSKAYGLAALRVGYGLSTAVVADV 251 Query: 245 IEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPSQTNF 304 + R+PFN + L AAA AAL D+ ++A + N +G+QQ + GL PS+ NF Sbjct: 252 LNRVRQPFNVNSLALAAACAALKDEEYLAQSRQLNESGMQQLEAGFRELGLSWIPSKGNF 311 Query: 305 VLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEIL 360 + +D + A +FQ LL +G IVR G P LRITIG +N L L ++L Sbjct: 312 ICVDLGQVAAPVFQGLLREGVIVRPVANYGMPNHLRITIGLPAENSRFLEALTKVL 367 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: 376 Number of extensions: 14 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: 370 Length adjustment: 30 Effective length of query: 330 Effective length of database: 340 Effective search space: 112200 Effective search space used: 112200 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 PfGW456L13_2177 (Biosynthetic Aromatic amino acid aminotransferase beta (EC 2.6.1.57))
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.2872174.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-116 372.5 0.0 9.8e-116 372.4 0.0 1.0 1 FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 Domain annotation for each sequence (and alignments): >> FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 372.4 0.0 9.8e-116 9.8e-116 2 348 .. 11 365 .. 10 366 .. 0.98 Alignments for each domain: == domain 1 score: 372.4 bits; conditional E-value: 9.8e-116 TIGR01141 2 ekikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrY 52 + +++l+pY+pg arel + ++kL+snEnP+g +k+++a++++l++l+rY FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 11 PGVQQLSPYVPGkpvdelARELDLDpaSIIKLASNENPLGAGPKALAAIRDALAELTRY 69 679***************999999999******************************** PP TIGR01141 53 pdpqalelkealakylgveeenillgnGsdelielliraflepgdavlvleptysmYev 111 pd ++++lk+ la+++ ve ++++lgnGs++++el++ra+l pg +++++e+++++Y++ FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 70 PDGNGFALKSLLAEQCRVELDQVTLGNGSNDILELVARAYLAPGLNAVFSEHAFAVYPI 128 *********************************************************** PP TIGR01141 112 sakiagaevkevplkedgqedleavleaakekvklvflasPnnPtGnllkreeiekvle 170 +++ ga+ k vp+k++g +dl+a+l+a++ ++++vf+a+PnnPtG+++++e + ++l+ FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 129 ATQAVGAQAKVVPAKDWG-HDLPAMLAAIDANTRVVFIANPNNPTGTWFDAEALDEFLQ 186 *************99995.9*************************************** PP TIGR01141 171 ev.edalVVvDeAYieFsee...asvlellaeypnlvvlrTlSKafgLAglRvGyaian 225 v e++lVV+DeAYie++e ++ l++la ypnl+v+rT+SKa+gLA+lRvGy++++ FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 187 DVpEHVLVVLDEAYIEYAEGsdlPDGLDFLAAYPNLLVSRTFSKAYGLAALRVGYGLST 245 **99**************999999*********************************** PP TIGR01141 226 aeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkklegle 284 a ++++l++vr+p+nv+slal+aa+aal+d+++++++ + +++++++l++++++l gl+ FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 246 AVVADVLNRVRQPFNVNSLALAAACAALKDEEYLAQSRQLNESGMQQLEAGFREL-GLS 303 *******************************************************.8** PP TIGR01141 285 vyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerll 343 +++Sk+NF+ +++ + a+ +++ ll++g+ivR ++++ g+ +++lRit+G + en r+l FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 304 WIPSKGNFICVDLGQVAAPVFQGLLREGVIVRPVANY-GM-PNHLRITIGLPAENSRFL 360 *************************************.96.****************** PP TIGR01141 344 ealke 348 eal + FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2177 361 EALTK 365 **987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (370 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: 23.46 // [ok]
This GapMind analysis is from Jul 25 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