Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate Pf6N2E2_2519 Biosynthetic Aromatic amino acid aminotransferase beta (EC 2.6.1.57)
Query= metacyc::BSU22620-MONOMER (360 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519 Length = 370 Score = 275 bits (704), Expect = 1e-78 Identities = 152/356 (42%), Positives = 211/356 (59%), Gaps = 3/356 (0%) Query: 7 LKQLKPYQPGKPIEAVKSEYGLD--KVVKLASNENPYGCSEAAKEALHHEIQQLALYPDG 64 ++QL PY PGKP++ + E LD +VKLASNENP G S A A+ E+ +L YPDG Sbjct: 13 VQQLSPYVPGKPVDELARELDLDPASIVKLASNENPLGASPKALAAIRDELAELTRYPDG 72 Query: 65 YSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNAVI 124 AL++ L++ V + GNGS++I++++ RA+L N V + F Y Sbjct: 73 NGFALKSLLAERCGVELNQVTLGNGSNDILELVARAYLAPGLNAVFSEHAFAVYPIATQA 132 Query: 125 EGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERVPSR 184 GA+ + + D HDL AML AID T+VV+I +PNNPTGT+ L FL+ VP+ Sbjct: 133 VGADAHVVPAK-DWGHDLPAMLAAIDANTRVVFIANPNNPTGTWFDAQALDDFLQDVPAH 191 Query: 185 VLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENLIRQ 244 VLVVLDEAY EY D P+ + L+ Y NL++ RTFSKAYGLA+LRVGYG++ + Sbjct: 192 VLVVLDEAYIEYAEGSDLPDGLDFLAAYPNLLVSRTFSKAYGLASLRVGYGLSTAVVADV 251 Query: 245 IEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPSQTNF 304 + R+PFN + AAA AAL D+A++A N AG+QQ + GL PS+ NF Sbjct: 252 LNRVRQPFNVNSFALAAACAALQDEAYLAESRRLNAAGMQQLEAGFRELGLSWIPSKGNF 311 Query: 305 VLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEIL 360 + +D R A ++Q LL +G IVR G P LR+TIG +N L L+++L Sbjct: 312 ICVDLGRVAAPVYQGLLREGVIVRPVVNYGMPNHLRVTIGLPAENNRFLEALSKVL 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: 361 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 Pf6N2E2_2519 (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.18985.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-115 370.6 0.0 3.8e-115 370.4 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519 Biosynthetic Aromatic amino acid Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519 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 ! 370.4 0.0 3.8e-115 3.8e-115 2 348 .. 11 365 .. 10 366 .. 0.98 Alignments for each domain: == domain 1 score: 370.4 bits; conditional E-value: 3.8e-115 TIGR01141 2 ekikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqa 57 + +++l+pY+pg arel + +vkL+snEnP+g s+k+++a+++el++l+rYpd ++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519 11 PGVQQLSPYVPGkpvdelARELDLDpaSIVKLASNENPLGASPKALAAIRDELAELTRYPDGNG 74 679***************999999999************************************* PP TIGR01141 58 lelkealakylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevk 121 ++lk+ la+++gve ++++lgnGs++++el++ra+l pg +++++e+++++Y++ +++ ga+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519 75 FALKSLLAERCGVELNQVTLGNGSNDILELVARAYLAPGLNAVFSEHAFAVYPIATQAVGADAH 138 **************************************************************** PP TIGR01141 122 evplkedgqedleavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYi 184 vp+k++g +dl+a+l+a++ ++++vf+a+PnnPtG++++++ + ++l+ v +++lVV+DeAYi lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519 139 VVPAKDWG-HDLPAMLAAIDANTRVVFIANPNNPTGTWFDAQALDDFLQDVpAHVLVVLDEAYI 201 ***99995.9*****************************************88*********** PP TIGR01141 185 eFsee...asvlellaeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvssla 245 e++e ++ l++la ypnl+v+rT+SKa+gLA+lRvGy++++a ++++l++vr+p+nv+s a lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519 202 EYAEGsdlPDGLDFLAAYPNLLVSRTFSKAYGLASLRVGYGLSTAVVADVLNRVRQPFNVNSFA 265 ***999999******************************************************* PP TIGR01141 246 leaavaalrdsdkiektveevkkererlleelkkleglevyeSkaNFvlikvkedaeelleall 309 l+aa+aal+d+++++++ + +++++++l++++++l gl++++Sk+NF+ +++ + a+ +++ ll lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519 266 LAAACAALQDEAYLAESRRLNAAGMQQLEAGFREL-GLSWIPSKGNFICVDLGRVAAPVYQGLL 328 ***********************************.8*************************** PP TIGR01141 310 ekgiivRdlksaeglleeclRitvGtreenerllealke 348 ++g+ivR + ++ g+ +++lR+t+G + en+r+leal++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2519 329 REGVIVRPVVNY-GM-PNHLRVTIGLPAENNRFLEALSK 365 **********99.96.********************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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.73 // [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