Align Histidinol-phosphate aminotransferase; EC 2.6.1.9 (characterized, see rationale)
to candidate WP_018232412.1 THITHI_RS0107235 histidinol-phosphate transaminase
Query= uniprot:A0A2R7PAQ8 (373 letters) >NCBI__GCF_000378965.1:WP_018232412.1 Length = 363 Score = 291 bits (744), Expect = 3e-83 Identities = 166/357 (46%), Positives = 226/357 (63%), Gaps = 14/357 (3%) Query: 15 IRPDVRAMHSYVVQPSTGMLKMDAMENPFRLPAHLQAALGQRLGSVALNRYPGDRIADLK 74 IRP +RA+ +Y V +TG++K+DAMENP+ P L A + L VALNRYP R L Sbjct: 13 IRPGIRALAAYHVPDATGLVKLDAMENPYHWPRELVDAWLEVLRGVALNRYPDPRSPQLI 72 Query: 75 AALAQYAGMPEGYGIVLGNGSDELITLLALACAQPGTGQRATMLAPMPGFVMYPLSAQLQ 134 L + AG+P ++LGNGSDELI ++ +A A+PG +++ P FVMY + Sbjct: 73 DTLRRVAGIPAEQSVILGNGSDELIQVIIMALAEPGR----VVMSVEPSFVMYRMITGYA 128 Query: 135 GLDFVGVPLTPDFELDEPAMLAAIGQHRPAITYIAYPNNPTATLWDEGAVQRIIDAAGAQ 194 +++VGVPL DF LD PA LAA+ HRPA+ ++AYPNNPT + V+ +I AA Sbjct: 129 DMNYVGVPLGEDFALDTPAFLAAMKAHRPAVVFLAYPNNPTGNRFSRPDVEAVIRAAP-- 186 Query: 195 GGIVVMDEAYQPFASRTWIDRMRAEPARNAHVLLMRTLSKFGLAGVRLGYLIGPSAFVSE 254 G+VV+DEAY PFA D ++ R ++++MRT+SK GLAG+RLGYL GP+A++SE Sbjct: 187 -GLVVLDEAYAPFAD----DSFLSDLGRYPNLVVMRTVSKQGLAGLRLGYLCGPAAWLSE 241 Query: 255 IDKVRPPYNVSVLNCEAALFALEHAEVFAAQAAEIRVERATLIAALRQMPGVEKCWDSEA 314 DKVR PYN++VL +A FAL H V QAA IR +R TL AL +PGV + SEA Sbjct: 242 FDKVRLPYNINVLTQASADFALAHHHVLDEQAAAIRRDRETLARALAGLPGVTP-YPSEA 300 Query: 315 NMVLIRV--ADSAKAYEGMKNRKVLVKNVSTMHPLLANCLRLTVGNAEDNAQMLAAL 369 N +L RV ++G+K VL+KN+S L +CLR+TVG E+N + LAAL Sbjct: 301 NFILFRVPAGRGDAVFQGLKEAGVLIKNLSGQGGALTDCLRVTVGRPEENERFLAAL 357 Lambda K H 0.321 0.134 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: 411 Number of extensions: 21 Number of successful extensions: 5 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: 373 Length of database: 363 Length adjustment: 30 Effective length of query: 343 Effective length of database: 333 Effective search space: 114219 Effective search space used: 114219 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 (21.9 bits) S2: 49 (23.5 bits)
Align candidate WP_018232412.1 THITHI_RS0107235 (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.304672.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-103 330.1 0.0 7.7e-103 330.0 0.0 1.0 1 NCBI__GCF_000378965.1:WP_018232412.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000378965.1:WP_018232412.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 330.0 0.0 7.7e-103 7.7e-103 1 348 [. 14 359 .. 14 360 .. 0.96 Alignments for each domain: == domain 1 score: 330.0 bits; conditional E-value: 7.7e-103 TIGR01141 1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk..klhrYpdpqalelkealakylgve 71 r+ i++l++Y+ + + ++ vkL+++EnP+ ++++++a+ e l+ l+rYpdp + +l +l++++g+ NCBI__GCF_000378965.1:WP_018232412.1 14 RPGIRALAAYHVP---D-ATGLVKLDAMENPYHWPRELVDAWLEVLRgvALNRYPDPRSPQLIDTLRRVAGIP 82 6789999999994...2.2368*************************999*********************76 PP TIGR01141 72 een.illgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavle.aake 142 +e+ ++lgnGsdeli+++i+a++epg+ v+ +ep++ mY++++ a+++++ vpl ed+ d++a+l+ +++ NCBI__GCF_000378965.1:WP_018232412.1 83 AEQsVILGNGSDELIQVIIMALAEPGRVVMSVEPSFVMYRMITGYADMNYVGVPLGEDFALDTPAFLAaMKAH 155 6554*************************************************************99978999 PP TIGR01141 143 kvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLA 215 ++ +vfla+PnnPtGn ++r ++e+v+ ++ +lVV+DeAY F+++ s+l+ l +ypnlvv+rT+SK LA NCBI__GCF_000378965.1:WP_018232412.1 156 RPAVVFLAYPNNPTGNRFSRPDVEAVIRAA-PGLVVLDEAYAPFADD-SFLSDLGRYPNLVVMRTVSKQG-LA 225 *****************************8.9**************8.********************87.** PP TIGR01141 216 glRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeS 288 glR+Gy+ + a++ ++++kvr pyn+++l+++ a al +++ + ++ ++++++re l +l+ l+g+ y+S NCBI__GCF_000378965.1:WP_018232412.1 226 GLRLGYLCGPAAWLSEFDKVRLPYNINVLTQASADFALAHHHVLDEQAAAIRRDRETLARALAGLPGVTPYPS 298 ************************************************************************* PP TIGR01141 289 kaNFvlikvke.daeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348 +aNF+l++v++ +++++ l+e+g+++++l+ + g l++clR+tvG +eener+l+al + NCBI__GCF_000378965.1:WP_018232412.1 299 EANFILFRVPAgRGDAVFQGLKEAGVLIKNLSGQGGALTDCLRVTVGRPEENERFLAALGR 359 **********999*********************************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (363 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 14.77 // [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