Align Histidinol-phosphate aminotransferase 3; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 3 (uncharacterized)
to candidate SMa0387 SMa0387 histidinol-phosphate aminotransferase
Query= curated2:Q930J0 (370 letters) >FitnessBrowser__Smeli:SMa0387 Length = 370 Score = 732 bits (1889), Expect = 0.0 Identities = 370/370 (100%), Positives = 370/370 (100%) Query: 1 MAIPSRPIREEIRSIAPYNAGLTLEEVRAKYHVDEVAKLSSNENPLGPSPALRRLFPDIG 60 MAIPSRPIREEIRSIAPYNAGLTLEEVRAKYHVDEVAKLSSNENPLGPSPALRRLFPDIG Sbjct: 1 MAIPSRPIREEIRSIAPYNAGLTLEEVRAKYHVDEVAKLSSNENPLGPSPALRRLFPDIG 60 Query: 61 ELARLYPDPQGRALCARLAASFDVENNQVILGNGSEDLIAVICRSVVRAGDTVVTLYPSF 120 ELARLYPDPQGRALCARLAASFDVENNQVILGNGSEDLIAVICRSVVRAGDTVVTLYPSF Sbjct: 61 ELARLYPDPQGRALCARLAASFDVENNQVILGNGSEDLIAVICRSVVRAGDTVVTLYPSF 120 Query: 121 PLHEDYTTLMGGKVDRVTVTPDLSVDMDALLAAIARKPRMLMFSNPMNPVGSWLTPLQLA 180 PLHEDYTTLMGGKVDRVTVTPDLSVDMDALLAAIARKPRMLMFSNPMNPVGSWLTPLQLA Sbjct: 121 PLHEDYTTLMGGKVDRVTVTPDLSVDMDALLAAIARKPRMLMFSNPMNPVGSWLTPLQLA 180 Query: 181 KVVAALDPETLIVVDEAYAEYAAGDDYPSAAEVLKVTGLNWVVLRTFSKAYGLAGLRIGY 240 KVVAALDPETLIVVDEAYAEYAAGDDYPSAAEVLKVTGLNWVVLRTFSKAYGLAGLRIGY Sbjct: 181 KVVAALDPETLIVVDEAYAEYAAGDDYPSAAEVLKVTGLNWVVLRTFSKAYGLAGLRIGY 240 Query: 241 GIVSDGSLCDFFNRARTPFNTNAIAQVSALAAFDDTYHLNRSVELALVERERMKKELATM 300 GIVSDGSLCDFFNRARTPFNTNAIAQVSALAAFDDTYHLNRSVELALVERERMKKELATM Sbjct: 241 GIVSDGSLCDFFNRARTPFNTNAIAQVSALAAFDDTYHLNRSVELALVERERMKKELATM 300 Query: 301 GYRIAPSKCNFLFFDARTEATPVAEALLRRGVIVKPWKQPRFETYIRVSIGSPVENDHFI 360 GYRIAPSKCNFLFFDARTEATPVAEALLRRGVIVKPWKQPRFETYIRVSIGSPVENDHFI Sbjct: 301 GYRIAPSKCNFLFFDARTEATPVAEALLRRGVIVKPWKQPRFETYIRVSIGSPVENDHFI 360 Query: 361 HALKEVEAVG 370 HALKEVEAVG Sbjct: 361 HALKEVEAVG 370 Lambda K H 0.320 0.136 0.398 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: 576 Number of extensions: 5 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: 370 Length of database: 370 Length adjustment: 30 Effective length of query: 340 Effective length of database: 340 Effective search space: 115600 Effective search space used: 115600 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 SMa0387 SMa0387 (histidinol-phosphate aminotransferase)
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.22709.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-91 291.9 0.0 3.2e-91 291.7 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMa0387 SMa0387 histidinol-phosphate ami Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMa0387 SMa0387 histidinol-phosphate aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 291.7 0.0 3.2e-91 3.2e-91 1 349 [] 9 366 .. 9 366 .. 0.94 Alignments for each domain: == domain 1 score: 291.7 bits; conditional E-value: 3.2e-91 TIGR01141 1 rekikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelk.klhrYpdpqalelkealakylg 69 re+i++++pY++g ++ +ev kL+snEnP+gps+++ +l + ++Ypdpq+ +l ++la+ ++ lcl|FitnessBrowser__Smeli:SMa0387 9 REEIRSIAPYNAGltleevRAKYHVDEVAKLSSNENPLGPSPAL-RRLFPDIGeLARLYPDPQGRALCARLAASFD 83 799************999766777779**************955.5566666625567****************** PP TIGR01141 70 veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaakekvk 145 ve+++++lgnGs++li +++r+++ gd+v++l p++ ++e ++++ g +v v ++ d + d++a+l+a+++k++ lcl|FitnessBrowser__Smeli:SMa0387 84 VENNQVILGNGSEDLIAVICRSVVRAGDTVVTLYPSFPLHEDYTTLMGGKVDRVTVTPDLSVDMDALLAAIARKPR 159 ***********************************************************99*************** PP TIGR01141 146 lvflasPnnPtGnllkreeiekvleeve.dalVVvDeAYieFsee...asvlellaeyp.nlvvlrTlSKafgLAg 216 + + +P nP+G++l+ ++ kv+++ ++l+VvDeAY e++ +s++e+l+ n vvlrT+SKa+gLAg lcl|FitnessBrowser__Smeli:SMa0387 160 MLMFSNPMNPVGSWLTPLQLAKVVAALDpETLIVVDEAYAEYAAGddyPSAAEVLKVTGlNWVVLRTFSKAYGLAG 235 ***************************66**************98788999999998888**************** PP TIGR01141 217 lRvGyaian.aeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSkaN 291 lR+Gy+i++ ++ + +++ r+p+n++ +a+ a+aa +d +++++ve erer+++el+++ g ++ +Sk N lcl|FitnessBrowser__Smeli:SMa0387 236 LRIGYGIVSdGSLCDFFNRARTPFNTNAIAQVSALAAFDDTYHLNRSVELALVERERMKKELATM-GYRIAPSKCN 310 *****9875169*****************************************************.8********* PP TIGR01141 292 FvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllealkei 349 F++++++++a+ ++eall++g+iv+ k+ e+++R+++G++ en+++++alke+ lcl|FitnessBrowser__Smeli:SMa0387 311 FLFFDARTEATPVAEALLRRGVIVKPWKQP--RFETYIRVSIGSPVENDHFIHALKEV 366 ***************************944..57*********************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (370 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: 00:00:00.01 # Mc/sec: 10.78 // [ok]
This GapMind analysis is from Apr 09 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