Align Histidinol-phosphate aminotransferase 1; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 1 (uncharacterized)
to candidate WP_017599139.1 D471_RS0113730 histidinol-phosphate transaminase
Query= curated2:Q46Y48 (376 letters) >NCBI__GCF_000341125.1:WP_017599139.1 Length = 360 Score = 233 bits (594), Expect = 6e-66 Identities = 138/326 (42%), Positives = 183/326 (56%), Gaps = 9/326 (2%) Query: 45 VKLASNENPLGMPESAKHAAAAAIAELGRYPDSNGFELKAALSTKLGVPQDWLTLGNGSN 104 +KL+SNE+P G S + A A A AEL RYPD L L+ LGVP++ + LG GS Sbjct: 34 IKLSSNESPFGPLPSVREAVAQASAELNRYPDPGATALVTELARHLGVPEEHVALGAGSV 93 Query: 105 DILELAAHALVTPGQSIVYAEYSFAVYALATQEIGARAIVVKARDYGHDLDAMAAAITSD 164 +L+ A+ PG +VYA SF Y L + G ++ V RD HDLDA+A AIT Sbjct: 94 GLLQQLLEAVGEPGAEVVYAWRSFEAYPLLAELAGVTSVRVPLRDETHDLDAIADAITES 153 Query: 165 TRLVFIANPNNPTGTFVPAAALETFLAKVPAEVVVVLDEAYNEYLDDDQQYDSVAWVRRY 224 TR+V + NPNNPTGT VP L FL +VP V+V+LDEAY+EY+ D + D V R Sbjct: 154 TRMVLVCNPNNPTGTTVPKGELLAFLDRVPEHVLVILDEAYHEYVRDPRVPDGVELYRDR 213 Query: 225 PNLLVSRTFSKAYGLAGLRIGYAVAQPELTDLLNRIRQPFNVNSVAQAAAVAALGDTAFL 284 PN+ V RTFSKAYGLA +R+GY VA P + + PF VN +AQAA +A+L L Sbjct: 214 PNVAVLRTFSKAYGLAAVRLGYLVAHPHVAAAARKTLVPFAVNHLAQAAGIASLAARDEL 273 Query: 285 QRSAELNRAGKAQLVEAFSRLGLEFVASSGNFVLVRVGDDD-DAGARVNVALLRQGVIVR 343 E + ++ +A G + NFV +RVG+D D A + GV VR Sbjct: 274 MERVEATVGERTRVRDALIASGWTVPPTEANFVWLRVGEDTLDFAAE----CAKVGVSVR 329 Query: 344 PVGNYGMPRWLRVTIGLPDENAAFIA 369 P G RV++G P+EN F++ Sbjct: 330 PFEGEG----ARVSLGTPEENDVFLS 351 Lambda K H 0.318 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: 336 Number of extensions: 9 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: 376 Length of database: 360 Length adjustment: 30 Effective length of query: 346 Effective length of database: 330 Effective search space: 114180 Effective search space used: 114180 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_017599139.1 D471_RS0113730 (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.16166.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-91 292.1 0.0 2.9e-91 291.9 0.0 1.0 1 lcl|NCBI__GCF_000341125.1:WP_017599139.1 D471_RS0113730 histidinol-phosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000341125.1:WP_017599139.1 D471_RS0113730 histidinol-phosphate transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 291.9 0.0 2.9e-91 2.9e-91 2 345 .. 12 352 .. 11 356 .. 0.97 Alignments for each domain: == domain 1 score: 291.9 bits; conditional E-value: 2.9e-91 TIGR01141 2 ekikklepYqpgarelgek.evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylg 69 ++++ +Y+pg + +g + +kL+snE+Pfgp ++v+ea+ ++ ++l+rYpdp a++l ++la++lg lcl|NCBI__GCF_000341125.1:WP_017599139.1 12 SVLESIPAYKPGRKVVGPDgRSIKLSSNESPFGPLPSVREAVAQASAELNRYPDPGATALVTELARHLG 80 5688999*****888888899************************99********************** PP TIGR01141 70 veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavle 138 v ee ++lg+Gs +l++ l++a+ epg++v+++ +++ Y++ a++ag+ + vpl+++ ++dl+a+++ lcl|NCBI__GCF_000341125.1:WP_017599139.1 81 VPEEHVALGAGSVGLLQQLLEAVGEPGAEVVYAWRSFEAYPLLAELAGVTSVRVPLRDE-THDLDAIAD 148 **********************************************************9.6******** PP TIGR01141 139 aakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlv 203 a++e++++v +++PnnPtG+ + + e+ ++l++v e++lV++DeAY e+ ++ ++ +el +++pn++ lcl|NCBI__GCF_000341125.1:WP_017599139.1 149 AITESTRMVLVCNPNNPTGTTVPKGELLAFLDRVpEHVLVILDEAYHEYVRDprvPDGVELYRDRPNVA 217 **********************************99****************9999************* PP TIGR01141 204 vlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkerer 272 vlrT+SKa+gLA++R+Gy++a+++++ a +k p+ v+ la++a++a+l +d+++++ve+ er+r lcl|NCBI__GCF_000341125.1:WP_017599139.1 218 VLRTFSKAYGLAAVRLGYLVAHPHVAAAARKTLVPFAVNHLAQAAGIASLAARDELMERVEATVGERTR 286 ********************************************************************* PP TIGR01141 273 lleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreener 341 + ++l + g v + +aNFv ++v ed +++ + + g+ vR ++ g R++ Gt+een+ lcl|NCBI__GCF_000341125.1:WP_017599139.1 287 VRDALIAS-GWTVPPTEANFVWLRVGEDTLDFAAECAKVGVSVRPFEGE-G-----ARVSLGTPEENDV 348 ******98.89***********************************966.6.....5************ PP TIGR01141 342 llea 345 +l + lcl|NCBI__GCF_000341125.1:WP_017599139.1 349 FLSV 352 *987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (360 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: 9.79 // [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