Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_089323092.1 CHB58_RS05420 histidinol-phosphate transaminase
Query= metacyc::BSU22620-MONOMER (360 letters) >NCBI__GCF_900188395.1:WP_089323092.1 Length = 372 Score = 282 bits (721), Expect = 1e-80 Identities = 152/361 (42%), Positives = 221/361 (61%), Gaps = 3/361 (0%) Query: 2 RIKEHLKQLKPYQPGKPIEAVKSEYGLDKVVKLASNENPYGCSEAAKEALHHEIQQLALY 61 ++ EH+KQ+ Y+PGKPIE ++ E G+ +VKLASNENP G S +A+ +++ L Y Sbjct: 3 KLPEHIKQVHVYEPGKPIEELEKELGIKNIVKLASNENPLGPSPKGVQAIIEDLKNLHRY 62 Query: 62 PDGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQYKHN 121 PDG S L+ L+KHLNV ++ G GS+E + II RA+L N V + +F Y Sbjct: 63 PDGNSYYLKNALAKHLNVKPENIFVGLGSNEALDIISRAYLRPGVNAVYSEKSFAVYPIV 122 Query: 122 AVIEGAEVREIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELLAFLERV 181 + GAE + + ++ + DL A L+AID++T VV++ +PNNPTGT S+ E FL+ Sbjct: 123 VQLAGAEHKVVKVKDNYYMDLKAHLDAIDDKTAVVFLANPNNPTGTAFSKKEFEEFLKEF 182 Query: 182 PSRVLVVLDEAYYEYVTAE--DYPETVPLLSKYSNLMILRTFSKAYGLAALRVGYGIADE 239 P VL+VLDEAYYEY D V + + N+++ RTFSK YGLA LR+GY +A+E Sbjct: 183 PDDVLLVLDEAYYEYAVGAGFDIENGVEYIYE-KNMLVTRTFSKIYGLAGLRLGYAVANE 241 Query: 240 NLIRQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTHGLKCYP 299 +I + R+PFN +R Q A +AAL+D+ FI N G + Y + GLK P Sbjct: 242 EIIADMNRIRQPFNVTRPAQVAGVAALEDKMFIKQSQVVNEEGKKYLYKEFEKLGLKYVP 301 Query: 300 SQTNFVLIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEEILAILAEI 359 + NF+L+D P E+F+ LL KG IVR+ + GFPT +R+TIGT ++N + L E+ Sbjct: 302 TFANFILVDTGFPTREVFKRLLHKGVIVRAMDGYGFPTCIRVTIGTMKENIVFIDKLREV 361 Query: 360 L 360 + Sbjct: 362 I 362 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: 379 Number of extensions: 18 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: 372 Length adjustment: 30 Effective length of query: 330 Effective length of database: 342 Effective search space: 112860 Effective search space used: 112860 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_089323092.1 CHB58_RS05420 (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.26651.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-111 357.0 0.2 5.1e-111 356.8 0.2 1.0 1 lcl|NCBI__GCF_900188395.1:WP_089323092.1 CHB58_RS05420 histidinol-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900188395.1:WP_089323092.1 CHB58_RS05420 histidinol-phosphate transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 356.8 0.2 5.1e-111 5.1e-111 2 349 .] 6 361 .. 5 361 .. 0.97 Alignments for each domain: == domain 1 score: 356.8 bits; conditional E-value: 5.1e-111 TIGR01141 2 ekikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkeal 64 e+ik+++ Y+pg ++elg+k++vkL+snEnP+gps+k ++a+ e lk+lhrYpd +++ lk+al lcl|NCBI__GCF_900188395.1:WP_089323092.1 6 EHIKQVHVYEPGkpieelEKELGIKNIVKLASNENPLGPSPKGVQAIIEDLKNLHRYPDGNSYYLKNAL 74 689****************************************************************** PP TIGR01141 65 akylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedl 133 ak+l+v++eni++g Gs+e+++++ ra+l pg +++++e ++++Y++++++agae k v++k++ +dl lcl|NCBI__GCF_900188395.1:WP_089323092.1 75 AKHLNVKPENIFVGLGSNEALDIISRAYLRPGVNAVYSEKSFAVYPIVVQLAGAEHKVVKVKDNYYMDL 143 ****************************************************************99*** PP TIGR01141 134 eavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee.....asvlell 196 +a l+a+++k+ +vfla+PnnPtG+ ++++e+e++l+e d+l V+DeAY+e++ ++ +e++ lcl|NCBI__GCF_900188395.1:WP_089323092.1 144 KAHLDAIDDKTAVVFLANPNNPTGTAFSKKEFEEFLKEFpDDVLLVLDEAYYEYAVGagfdiENGVEYI 212 ***************************************78**************98887777777777 PP TIGR01141 197 aeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektvee 265 e n++v+rT+SK++gLAglR+Gya+an+eii ++++r+p+nv+++a+ a+vaal+d+ +i+++ lcl|NCBI__GCF_900188395.1:WP_089323092.1 213 YE-KNMLVTRTFSKIYGLAGLRLGYAVANEEIIADMNRIRQPFNVTRPAQVAGVAALEDKMFIKQSQVV 280 76.5999************************************************************** PP TIGR01141 266 vkkererlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvG 334 +++++++l++e++kl gl++++ aNF+l+++ + +e++++ll+kg+ivR + + g+ ++c+R+t+G lcl|NCBI__GCF_900188395.1:WP_089323092.1 281 NEEGKKYLYKEFEKL-GLKYVPTFANFILVDTGFPTREVFKRLLHKGVIVRAMDGY-GF-PTCIRVTIG 346 ***************.8***************99**********************.86.********* PP TIGR01141 335 treenerllealkei 349 t +en +++ l+e+ lcl|NCBI__GCF_900188395.1:WP_089323092.1 347 TMKENIVFIDKLREV 361 ***********9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (372 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: 8.08 // [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