Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_018231479.1 THITHI_RS0102420 histidinol-phosphate transaminase
Query= metacyc::BSU22620-MONOMER (360 letters) >NCBI__GCF_000378965.1:WP_018231479.1 Length = 373 Score = 291 bits (744), Expect = 2e-83 Identities = 158/359 (44%), Positives = 218/359 (60%), Gaps = 5/359 (1%) Query: 7 LKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQQLALYPDGYS 66 ++ L PYQPGKPI+ ++ E G+ + VKLASNENP G A +A ++ +ALYPDG Sbjct: 13 VQNLTPYQPGKPIDELERELGIRESVKLASNENPLGPGVRALDAARAQLSGVALYPDGNG 72 Query: 67 AALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNAVIEG 126 AL+ RL+++LNV T + GNGS+EI+++I RAFL N V +A F Y G Sbjct: 73 FALKRRLAEYLNVDATRITLGNGSNEILELIARAFLAPGRNAVFSAHAFAVYPIVVQAVG 132 Query: 127 AEVR-EIALRPDG----SHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERV 181 AE R +A PD HDLDAM ID T+VV++ +PNNPTGT+ E + AFL+RV Sbjct: 133 AEARVAVANGPDHVLPWGHDLDAMAALIDGDTRVVFVANPNNPTGTWLDEASVHAFLKRV 192 Query: 182 PSRVLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENL 241 P L V+DEAY+EY + YP+ L + NL++ RTFSK +GLA LR+GYG++ E + Sbjct: 193 PEDTLAVMDEAYFEYAEVDGYPDATRWLDAFPNLIVTRTFSKIHGLAGLRIGYGVSGEAV 252 Query: 242 IRQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPSQ 301 + R+PFNT+ L QAAA+AALDD + V+ N GL+Q GL PS Sbjct: 253 ADILNRVRQPFNTNSLAQAAALAALDDADHVRRSVQVNREGLRQLTAACGQRGLGFIPSV 312 Query: 302 TNFVLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEIL 360 NF+ ID R A +++ALL +G IVR G P LR+T+G + +N + L ++L Sbjct: 313 GNFLSIDVGREAAPVYEALLRQGVIVRPIAGYGLPNHLRVTVGREHENRRFIDALDKVL 371 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: 360 Number of extensions: 15 Number of successful extensions: 2 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: 373 Length adjustment: 30 Effective length of query: 330 Effective length of database: 343 Effective search space: 113190 Effective search space used: 113190 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_018231479.1 THITHI_RS0102420 (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.281266.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-111 356.7 0.0 6.5e-111 356.5 0.0 1.0 1 NCBI__GCF_000378965.1:WP_018231479.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000378965.1:WP_018231479.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 356.5 0.0 6.5e-111 6.5e-111 3 348 .. 12 369 .. 10 370 .. 0.98 Alignments for each domain: == domain 1 score: 356.5 bits; conditional E-value: 6.5e-111 TIGR01141 3 kikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylg 69 +++l+pYqpg +relg+ e vkL+snEnP+gp ++++a++++l+ + +Ypd ++++lk++la+yl+ NCBI__GCF_000378965.1:WP_018231479.1 12 GVQNLTPYQPGkpidelERELGIRESVKLASNENPLGPGVRALDAARAQLSGVALYPDGNGFALKRRLAEYLN 84 599********************************************************************** PP TIGR01141 70 veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplked.....gqedleavl 137 v+++ i+lgnGs+e++el++rafl pg++++++ +++++Y++++++ gae + + ++ + +dl+a++ NCBI__GCF_000378965.1:WP_018231479.1 85 VDATRITLGNGSNEILELIARAFLAPGRNAVFSAHAFAVYPIVVQAVGAEARVAVANGPdhvlpWGHDLDAMA 157 **************************************************9877666545899999******* PP TIGR01141 138 eaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlvvlr 206 + ++ ++++vf+a+PnnPtG++l+++ + ++l++v ed+l+V+DeAY e++e ++++ +l +pnl+v+r NCBI__GCF_000378965.1:WP_018231479.1 158 ALIDGDTRVVFVANPNNPTGTWLDEASVHAFLKRVpEDTLAVMDEAYFEYAEVdgyPDATRWLDAFPNLIVTR 230 ***********************************99***************99999**************** PP TIGR01141 207 TlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkk 279 T+SK++gLAglR+Gy+++ ++++++l++vr+p+n++sla++aa+aal+d+d+++++v+ ++++ ++l++++ + NCBI__GCF_000378965.1:WP_018231479.1 231 TFSKIHGLAGLRIGYGVSGEAVADILNRVRQPFNTNSLAQAAALAALDDADHVRRSVQVNREGLRQLTAACGQ 303 ************************************************************************9 PP TIGR01141 280 leglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348 gl ++S +NF+ i+v ++a+ ++eall++g+ivR ++ + gl +++lR+tvG ++en+r+++al++ NCBI__GCF_000378965.1:WP_018231479.1 304 R-GLGFIPSVGNFLSIDVGREAAPVYEALLRQGVIVRPIAGY-GL-PNHLRVTVGREHENRRFIDALDK 369 9.8***************************************.85.********************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (373 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: 17.41 // [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