Align histidinol-phosphate aminotransferase; tyrosine/phenylalanine aminotransferase (promiscuous) (EC 2.6.1.1; EC 2.6.1.9) (characterized)
to candidate WP_013553263.1 NITSA_RS01515 histidinol-phosphate transaminase
Query= metacyc::BSU22620-MONOMER (360 letters) >NCBI__GCF_000186245.1:WP_013553263.1 Length = 364 Score = 249 bits (635), Expect = 1e-70 Identities = 150/369 (40%), Positives = 216/369 (58%), Gaps = 15/369 (4%) Query: 1 MRIKEHLKQLKPYQPGKPIEAVKSEYGL--DKVVKLASNENPYGCSEAAKEALHHEIQQL 58 M+ + L ++K Y+ GKPIE V E+G+ D+VVKLASNENP G S EA+ + Sbjct: 1 MKFNKTLDKIKTYEAGKPIELVVREFGIEPDQVVKLASNENPLGTSPKVAEAIRANADKA 60 Query: 59 ALYPDGYSAALRTRLSKHLNVSETSLIFGNGSDEIIQIICRAFLNDKTNTVTAAPTFPQY 118 LYPD L+ LS+ V E SLI G GSD+I++ I RA LN++++ + + TF Y Sbjct: 61 HLYPDDSMFELKASLSRRFGVPEESLIIGAGSDQILEFISRAKLNEESSVLMSRVTFAMY 120 Query: 119 KHNAVIEGAEV---REIALRPDGSHDLDAMLEAIDEQTQVVWICSPNNPTGTYTSEGELL 175 A+ +GA + + RPD + M++A + VV++C+PNNPTG TS +L Sbjct: 121 SIYALQQGARILRTEDYRHRPD---EFIPMMQA--HRPDVVFLCTPNNPTGDATSREDLF 175 Query: 176 AFLERVPSRVLVVLDEAYYEYVTAED--YPETVPLLSKYSNLMILRTFSKAYGLAALRVG 233 A +E LVV+D AY EY A+D Y + +Y N + L TFSKAYGL +RVG Sbjct: 176 AIIEAADPETLVVVDGAYMEYAAAKDPAYRIDPAEILRYPNAVYLGTFSKAYGLGGMRVG 235 Query: 234 YGIADENLIRQIEPAREPFNTSRLGQAAAIAALDDQAFIASCVEQNNAGLQQYYDFAKTH 293 YGIA +I+ + R PFN + L AAAIAA +D+AF+ ++ + L +Y +A+ Sbjct: 236 YGIARPEIIQALMKLRPPFNITTLSLAAAIAANEDEAFVQKSLQIHRQELPRYEAYARER 295 Query: 294 GLKCYPSQTNFV--LIDFKRPADELFQALLEKGYIVRSGNALGFPTSLRITIGTKEQNEE 351 G + S TNF+ L D +R + E+ ALL +G IVR + G +LRITIGT EQN+ Sbjct: 296 GFEYIESYTNFITWLFDEERNSSEIADALLRRGVIVRDLASYGM-NALRITIGTPEQNDR 354 Query: 352 ILAILAEIL 360 + + + E+L Sbjct: 355 LFSAMDEVL 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: 354 Number of extensions: 19 Number of successful extensions: 8 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: 364 Length adjustment: 29 Effective length of query: 331 Effective length of database: 335 Effective search space: 110885 Effective search space used: 110885 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_013553263.1 NITSA_RS01515 (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.43427.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-104 333.8 0.0 5.9e-104 333.6 0.0 1.0 1 NCBI__GCF_000186245.1:WP_013553263.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000186245.1:WP_013553263.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 333.6 0.0 5.9e-104 5.9e-104 2 349 .] 5 362 .. 4 362 .. 0.93 Alignments for each domain: == domain 1 score: 333.6 bits; conditional E-value: 5.9e-104 TIGR01141 2 ekikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealak 66 + + k++ Y++g re+g++ +vvkL+snEnP+g+s+kv ea++++++k h+Ypd++++elk++l++ NCBI__GCF_000186245.1:WP_013553263.1 5 KTLDKIKTYEAGkpielvVREFGIEpdQVVKLASNENPLGTSPKVAEAIRANADKAHLYPDDSMFELKASLSR 77 56889999****999999999999999********************************************** PP TIGR01141 67 ylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavlea 139 ++gv ee++++g+Gsd+++e++ ra l+++ +vl++ +t++mY+++a ++ga++ ++ + e + NCBI__GCF_000186245.1:WP_013553263.1 78 RFGVPEESLIIGAGSDQILEFISRAKLNEESSVLMSRVTFAMYSIYALQQGARILRTEDYRH--RPDEFIPMM 148 ****************************************************9987765555..344444457 PP TIGR01141 140 akekvklvflasPnnPtGnllkreeiekvleeve.dalVVvDeAYieFsee......asvlellaeypnlvvl 205 +++++++vfl++PnnPtG +re++ +++e++ ++lVVvD AY+e++ + +e + +ypn v+l NCBI__GCF_000186245.1:WP_013553263.1 149 QAHRPDVVFLCTPNNPTGDATSREDLFAIIEAADpETLVVVDGAYMEYAAAkdpayrIDPAE-ILRYPNAVYL 220 9********************************66**************9966665444444.558******* PP TIGR01141 206 rTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelk 278 T+SKa+gL+g+RvGy+ia +eii+al+k+r+p+n+++l+l+aa+aa +d+++++k+++ ++e r+++ ++ NCBI__GCF_000186245.1:WP_013553263.1 221 GTFSKAYGLGGMRVGYGIARPEIIQALMKLRPPFNITTLSLAAAIAANEDEAFVQKSLQIHRQELPRYEAYAR 293 ************************************************************************* PP TIGR01141 279 kleglevyeSkaNFvlikvke..daeelleallekgiivRdlksaeglleeclRitvGtreenerllealkei 349 + g+e++eS++NF++ ++e +++e+++all++g+ivRdl+s+ g+ ++lRit+Gt+e+n+rl+ a++e+ NCBI__GCF_000186245.1:WP_013553263.1 294 ER-GFEYIESYTNFITWLFDEerNSSEIADALLRRGVIVRDLASY-GM--NALRITIGTPEQNDRLFSAMDEV 362 99.8***********988887779*******************99.87..*******************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (364 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: 00:00:00.00 # Mc/sec: 16.03 // [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