Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_013134239.1 ARNIT_RS02155 histidinol-phosphate transaminase
Query= curated2:Q7M7Y6 (367 letters) >NCBI__GCF_000092245.1:WP_013134239.1 Length = 368 Score = 456 bits (1173), Expect = e-133 Identities = 222/366 (60%), Positives = 286/366 (78%) Query: 1 MQFNPTLDSIKTYEAGKPIELVVREYGIKPQNVIKLASNENPFGASPKVIEAIAKEAVNA 60 M+FN L+++ TYEAGKPIELVVREYG+ P++VIKLASNENP+G S KV I + A N Sbjct: 1 MKFNEVLENVTTYEAGKPIELVVREYGVNPKDVIKLASNENPYGTSSKVTAKIQELAKNM 60 Query: 61 HRYPDDSMFELKEGLAGRFGVKSENVIIGSGSDQILEMAVHAKCNASSKVLMSKTTFAMY 120 YPDDSM+ELKE L +F V S NVIIGSGSDQI+E VHAKC SK+LM+KTTFAMY Sbjct: 61 FVYPDDSMYELKEALGKKFDVDSSNVIIGSGSDQIIEFCVHAKCEKDSKLLMAKTTFAMY 120 Query: 121 DVYSRQVGARILRTPSDQHHLGEFWEIYQKERPEILFLCLPNNPLGECLDREEVYDFLQK 180 ++Y +Q GA+I++T S H L +F +Y++ +++FLCLPNNPLGE +D ++VY+FL++ Sbjct: 121 EIYGKQTGAKIIKTESHTHDLAQFLALYKEHGADVIFLCLPNNPLGEAVDTKDVYEFLEQ 180 Query: 181 IDDETLVIVDGAYQEYAAFKDSQKRIDPKDLIERFPSSIFLGTFSKAFGLGGMRVGYGIA 240 ID ETLV+VDGAYQEYAA+KD KRI PKDLI +F + I+LGTFSKA+ LGGMRVGYGIA Sbjct: 181 IDSETLVVVDGAYQEYAAYKDENKRIVPKDLITKFSNCIYLGTFSKAYALGGMRVGYGIA 240 Query: 241 QPSIIQALMKMRAPFNITTLSLKAAIEALKESAYVEETIKENFKEMRRYEEFALAQGIDF 300 QP II+ L K+RAPFNITTL+L AAIEALK+ +V I +NF+EM RYEE+A ++G ++ Sbjct: 241 QPEIIKTLYKLRAPFNITTLTLAAAIEALKDEEFVTACIAKNFEEMTRYEEYAKSRGFEY 300 Query: 301 IPSYTNFITLLLKNRVDSSEFSQWLLERGLIVRNLKSYGINAIRITIGRSLENDRCFELM 360 IPSYTNFIT+ + ++ S E +Q LLE G+IVR+L YG NAIRITIG + +N + F ++ Sbjct: 301 IPSYTNFITIKMGDKFVSKEVAQKLLEVGIIVRDLTGYGQNAIRITIGTNEQNTKVFSVL 360 Query: 361 QEYLHQ 366 E L + Sbjct: 361 DEVLEK 366 Lambda K H 0.320 0.137 0.392 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: 452 Number of extensions: 17 Number of successful extensions: 1 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: 367 Length of database: 368 Length adjustment: 30 Effective length of query: 337 Effective length of database: 338 Effective search space: 113906 Effective search space used: 113906 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_013134239.1 ARNIT_RS02155 (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.1115.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-105 338.2 2.4 2.8e-105 338.0 2.4 1.0 1 lcl|NCBI__GCF_000092245.1:WP_013134239.1 ARNIT_RS02155 histidinol-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092245.1:WP_013134239.1 ARNIT_RS02155 histidinol-phosphate transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 338.0 2.4 2.8e-105 2.8e-105 2 349 .] 5 363 .. 4 363 .. 0.95 Alignments for each domain: == domain 1 score: 338.0 bits; conditional E-value: 2.8e-105 TIGR01141 2 ekikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelke 62 e +++++ Y++g re+g + +v+kL+snEnP+g+s kv+++++e +k++ Ypd++++elke lcl|NCBI__GCF_000092245.1:WP_013134239.1 5 EVLENVTTYEAGkpielvVREYGVNpkDVIKLASNENPYGTSSKVTAKIQELAKNMFVYPDDSMYELKE 73 5688999********999999999999****************************************** PP TIGR01141 63 alakylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqe 131 al k+++v+ n+++g Gsd++ie+ ++a +e+ + l+++ t++mYe++ k++ga++++++ +++ lcl|NCBI__GCF_000092245.1:WP_013134239.1 74 ALGKKFDVDSSNVIIGSGSDQIIEFCVHAKCEKDSKLLMAKTTFAMYEIYGKQTGAKIIKTESHTHDLA 142 ************************************************************999998544 PP TIGR01141 132 dleavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee......asvl 193 ++ a+ +++ ++++fl+ PnnP G+ ++++++ ++le+ +++lVVvD AY e++ lcl|NCBI__GCF_000092245.1:WP_013134239.1 143 QFLAL--YKEHGADVIFLCLPNNPLGEAVDTKDVYEFLEQIdSETLVVVDGAYQEYAAYkdenkrIVPK 209 44444..5999******************************66*************9887777666677 PP TIGR01141 194 ellaeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiekt 262 +l+++++n ++l T+SKa++L+g+RvGy+ia++eii++l k+rap+n+++l+l+aa++al+d++++ ++ lcl|NCBI__GCF_000092245.1:WP_013134239.1 210 DLITKFSNCIYLGTFSKAYALGGMRVGYGIAQPEIIKTLYKLRAPFNITTLTLAAAIEALKDEEFVTAC 278 99******************************************************************* PP TIGR01141 263 veevkkererlleelkkleglevyeSkaNFvlikvke..daeelleallekgiivRdlksaeglleecl 329 ++++ +e++r++e +k g+e+++S++NF++ik+ ++e++++lle giivRdl+ + g ++++ lcl|NCBI__GCF_000092245.1:WP_013134239.1 279 IAKNFEEMTRYEEYAKSR-GFEYIPSYTNFITIKMGDkfVSKEVAQKLLEVGIIVRDLTGY-G--QNAI 343 ***********9999988.8***************988889******************88.5..7*** PP TIGR01141 330 RitvGtreenerllealkei 349 Rit+Gt+e+n++++ +l+e+ lcl|NCBI__GCF_000092245.1:WP_013134239.1 344 RITIGTNEQNTKVFSVLDEV 363 ****************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (368 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.50 // [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