Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate Pf1N1B4_349 Biosynthetic Aromatic amino acid aminotransferase beta (EC 2.6.1.57)
Query= metacyc::BSU22620-MONOMER (360 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349 Length = 370 Score = 275 bits (704), Expect = 1e-78 Identities = 153/356 (42%), Positives = 209/356 (58%), Gaps = 3/356 (0%) Query: 7 LKQLKPYQPGKPIEAVKSEYGLD--KVVKLASNENPYGCSEAAKEALHHEIQQLALYPDG 64 ++QL PY PGKP++ + E LD +VKLASNENP G S A A+ + +L YPDG Sbjct: 13 VQQLSPYVPGKPVDELARELNLDPANIVKLASNENPLGASPKALAAIREALTELTRYPDG 72 Query: 65 YSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNAVI 124 AL+T L+ V + GNGS++I++++ RA+L N V +A F Y Sbjct: 73 NGFALKTLLADQCRVELNQVTLGNGSNDILELVARAYLAPGLNAVFSAHAFAVYPIVTQA 132 Query: 125 EGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERVPSR 184 GA+ + I + D HDL AML AID T+VV+I +PNNPTGT+ L FL+ VP+ Sbjct: 133 VGAQAKVIPAK-DWGHDLSAMLAAIDADTRVVFIANPNNPTGTWFDAQALDDFLQDVPAH 191 Query: 185 VLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENLIRQ 244 VLVVLDEAY EY D P+ + L+ Y NL++ RTFSKAYGLA+LRVGYG++ + Sbjct: 192 VLVVLDEAYIEYAEGSDLPDGLDYLAAYPNLLVSRTFSKAYGLASLRVGYGLSSAIVADV 251 Query: 245 IEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPSQTNF 304 + R+PFN + L AAA AAL D ++A N +G+QQ + GL PS+ NF Sbjct: 252 LNRVRQPFNVNSLALAAACAALQDVEYLAESRRLNESGMQQLQAGFRELGLSWIPSKGNF 311 Query: 305 VLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEIL 360 + +D R A +F+ LL +G IVR G P LRITIG +N L L +++ Sbjct: 312 ICVDLGRVAAPVFEGLLREGVIVRPVANYGMPNHLRITIGLPAENSRFLEALTKVM 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: 350 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: 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 Pf1N1B4_349 (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.15094.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-116 372.8 0.0 8.2e-116 372.6 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349 Biosynthetic Aromatic amino acid Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349 Biosynthetic Aromatic amino acid aminotransferase beta (EC 2.6.1.57) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 372.6 0.0 8.2e-116 8.2e-116 2 348 .. 11 365 .. 10 366 .. 0.98 Alignments for each domain: == domain 1 score: 372.6 bits; conditional E-value: 8.2e-116 TIGR01141 2 ekikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqal 58 + +++l+pY+pg arel + ++vkL+snEnP+g s+k+++a++e+l++l+rYpd +++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349 11 PGVQQLSPYVPGkpvdelARELNLDpaNIVKLASNENPLGASPKALAAIREALTELTRYPDGNGF 75 679***************999999999************************************** PP TIGR01141 59 elkealakylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkev 123 +lk+ la+++ ve ++++lgnGs++++el++ra+l pg +++++ +++++Y++++++ ga+ k + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349 76 ALKTLLADQCRVELNQVTLGNGSNDILELVARAYLAPGLNAVFSAHAFAVYPIVTQAVGAQAKVI 140 ***************************************************************** PP TIGR01141 124 plkedgqedleavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFs 187 p+k++g +dl a+l+a++ ++++vf+a+PnnPtG++++++ + ++l+ v +++lVV+DeAYie++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349 141 PAKDWG-HDLSAMLAAIDADTRVVFIANPNNPTGTWFDAQALDDFLQDVpAHVLVVLDEAYIEYA 204 *99995.9*****************************************88************** PP TIGR01141 188 ee...asvlellaeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaa 249 e ++ l++la ypnl+v+rT+SKa+gLA+lRvGy++++a ++++l++vr+p+nv+slal+aa lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349 205 EGsdlPDGLDYLAAYPNLLVSRTFSKAYGLASLRVGYGLSSAIVADVLNRVRQPFNVNSLALAAA 269 999999*********************************************************** PP TIGR01141 250 vaalrdsdkiektveevkkererlleelkkleglevyeSkaNFvlikvkedaeelleallekgii 314 +aal+d ++++++ + +++++++l++++++l gl++++Sk+NF+ +++ + a+ ++e ll++g+i lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349 270 CAALQDVEYLAESRRLNESGMQQLQAGFREL-GLSWIPSKGNFICVDLGRVAAPVFEGLLREGVI 333 *******************************.8******************************** PP TIGR01141 315 vRdlksaeglleeclRitvGtreenerllealke 348 vR ++++ g+ +++lRit+G + en r+leal + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_349 334 VRPVANY-GM-PNHLRITIGLPAENSRFLEALTK 365 *******.96.********************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.53 // [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