Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_013450221.1 CALNI_RS00445 histidinol-phosphate transaminase
Query= metacyc::BSU22620-MONOMER (360 letters) >NCBI__GCF_000183405.1:WP_013450221.1 Length = 366 Score = 264 bits (675), Expect = 2e-75 Identities = 145/359 (40%), Positives = 220/359 (61%), Gaps = 8/359 (2%) Query: 5 EHLKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQQLALYPDG 64 E + L PYQPGKPI+ ++ E G+ + +KLASNENP G S+ +A+ + ++ YP G Sbjct: 10 EKISSLIPYQPGKPIKELERELGVKEAIKLASNENPLGVSKKVIQAVTEALHEMNRYPLG 69 Query: 65 YSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHNAVI 124 + LR LS+ L+V +IFG GS+EII++ R F+ + + ++ AP+F Y A Sbjct: 70 DAFYLRQELSRFLDVPPHQIIFGTGSNEIIELAIRTFVKEGEHVLSYAPSFSVYGIIAQA 129 Query: 125 EGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERVPSR 184 G+ + + + D + + EA++ T++V++ +PNNPTG Y SE EL+ FL +P Sbjct: 130 AGSFCKWVPTKDRFKVDFNKLKEAVENSTRIVFLANPNNPTGVYFSEEELVDFLNYIPKE 189 Query: 185 VLVVLDEAYYEYVTAEDYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADENLIRQ 244 +V+LDEAY EYV A D+P+++ LL KY NL+I+RTFSKAYGLA R+GY I + I Sbjct: 190 TIVILDEAYVEYVDAPDFPDSLKLLKKYPNLIIMRTFSKAYGLAGFRIGYAIGHPDAIDM 249 Query: 245 IEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYPSQTNF 304 + R+PFN + + Q AAIAAL+D+ F+ + ++ N G Y K GL +Q NF Sbjct: 250 LNRVRQPFNVNMVAQIAAIAALEDREFVRNSIKINREGKAYLYKQFKELGLDYIETQANF 309 Query: 305 VLIDFKRPADELFQALLEKGYIVRSGNALGFPT---SLRITIGTKEQNEEILAILAEIL 360 +L++ D +F LL++G IVR LG PT +R++IGT ++NE + L +IL Sbjct: 310 ILVNVGDGKD-VFDRLLKEGVIVR---FLG-PTLKEYIRVSIGTPQENEVFITKLKKIL 363 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: 345 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: 366 Length adjustment: 29 Effective length of query: 331 Effective length of database: 337 Effective search space: 111547 Effective search space used: 111547 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_013450221.1 CALNI_RS00445 (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.32326.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-119 383.3 0.0 5.2e-119 383.1 0.0 1.0 1 lcl|NCBI__GCF_000183405.1:WP_013450221.1 CALNI_RS00445 histidinol-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183405.1:WP_013450221.1 CALNI_RS00445 histidinol-phosphate transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 383.1 0.0 5.2e-119 5.2e-119 2 349 .] 10 362 .. 9 362 .. 0.98 Alignments for each domain: == domain 1 score: 383.1 bits; conditional E-value: 5.2e-119 TIGR01141 2 ekikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkeal 64 eki++l pYqpg +relg ke +kL+snEnP+g+s+kv++a++e+l++++rYp +a+ l+++l lcl|NCBI__GCF_000183405.1:WP_013450221.1 10 EKISSLIPYQPGkpikelERELGVKEAIKLASNENPLGVSKKVIQAVTEALHEMNRYPLGDAFYLRQEL 78 6899***************************************************************** PP TIGR01141 65 akylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedl 133 +++l+v + +i++g Gs+e+iel ir+f+++g++vl p++s+Y ++a++ag +k vp+k+ ++ d+ lcl|NCBI__GCF_000183405.1:WP_013450221.1 79 SRFLDVPPHQIIFGTGSNEIIELAIRTFVKEGEHVLSYAPSFSVYGIIAQAAGSFCKWVPTKDRFKVDF 147 ********************************************************************* PP TIGR01141 134 eavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellae 198 ++++ea+++++++vfla+PnnPtG ++++ee++++l+ ++++V++DeAY+e+ + ++ l+ll++ lcl|NCBI__GCF_000183405.1:WP_013450221.1 148 NKLKEAVENSTRIVFLANPNNPTGVYFSEEELVDFLNYIpKETIVILDEAYVEYVDApdfPDSLKLLKK 216 ***************************************88***************999999******* PP TIGR01141 199 ypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevk 267 ypnl+++rT+SKa+gLAg R+Gyai++++ i++l++vr+p+nv+ +a+ aa+aal+d+++++++++ ++ lcl|NCBI__GCF_000183405.1:WP_013450221.1 217 YPNLIIMRTFSKAYGLAGFRIGYAIGHPDAIDMLNRVRQPFNVNMVAQIAAIAALEDREFVRNSIKINR 285 ********************************************************************* PP TIGR01141 268 kererlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtr 336 +++++l++++k+l gl+++e +aNF+l++v d ++++++ll++g+ivR l+ + l+e++R+++Gt+ lcl|NCBI__GCF_000183405.1:WP_013450221.1 286 EGKAYLYKQFKEL-GLDYIETQANFILVNVG-DGKDVFDRLLKEGVIVRFLGPT---LKEYIRVSIGTP 349 *************.8***************9.*******************944...7*********** PP TIGR01141 337 eenerllealkei 349 +ene +++ lk+i lcl|NCBI__GCF_000183405.1:WP_013450221.1 350 QENEVFITKLKKI 362 **********986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (366 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: 10.44 // [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