Align histidinol-phosphate aminotransferase [EC:2.6.1.9] (characterized)
to candidate CCNA_02306 CCNA_02306 histidinol-phosphate aminotransferase
Query= reanno::azobra:AZOBR_RS20485 (364 letters) >FitnessBrowser__Caulo:CCNA_02306 Length = 373 Score = 313 bits (803), Expect = 4e-90 Identities = 168/360 (46%), Positives = 222/360 (61%), Gaps = 7/360 (1%) Query: 8 PAPRPGILDIAPYVGGEH-----AGHIRLASNEGALGPSPRAVEAYRAAAGELHRYPDGG 62 P P+PGI+DI YVGG+ A ++L+SNE LG S +A +AYR A LH YPDG Sbjct: 14 PMPKPGIMDIHAYVGGKSKVEGIAHPVKLSSNENILGSSDKAKDAYRNAVDRLHIYPDGK 73 Query: 63 SAKLRKAIAERFGLDADRVVCGAGSDELIALLIRAYAGPGDEVLYSQHGFLMYPIGAKSV 122 + LR A+AER+ L+ +R+ G GSDE+ ALL + Y PGD ++ +HGF Y IGA++ Sbjct: 74 ANFLRAAVAERYKLEPERLTFGDGSDEIFALLCQVYLEPGDNIVQGEHGFAAYAIGARAC 133 Query: 123 GATPVQAPETNLTTDVDSLLAHVTPRTRLVFVANPNNPTGTYITADEMARLHAGLPENAI 182 A E N D+D ++ V RTRLVF+ANP NPTGT++T +E+ LHA LP + + Sbjct: 134 QGEVRMAKEVNHRVDIDEVIKCVDERTRLVFIANPANPTGTWLTGEEIRALHAALPPSVV 193 Query: 183 LVIDAAYAEYMNHNDYSAGQELVDRFPNVVMTRTFSKIFALGSVRLGWAYCPAGIADVLN 242 LV+D AYAE+ + + G EL NV++TRTFSKI L ++R+GW Y P I + Sbjct: 194 LVLDGAYAEFCSDPHFEDGLELARTAENVIVTRTFSKIHGLAALRVGWGYAPEHIIAPIE 253 Query: 243 RVRGPFNVSSAAQIAGVAALEDTAFLERSRSHNIEWREWFVQQVHGLGLKTHPSVTNFVL 302 R+R PFN S AQ A VAAL D F +RSR+ +WR W QQ+ GLGL+ PS NFVL Sbjct: 254 RIRPPFNTSIPAQEAAVAALFDDDFQDRSRALVEQWRPWLAQQLGGLGLEVTPSAANFVL 313 Query: 303 VDFAGQTAGKDDAEAARLFLKGRGILVRQMPAYGLPSCLRVTIGTEAEMREVVQALKDFL 362 F T GK A A FL +G LVR + Y LP +R+TIG E + R VV+ L F+ Sbjct: 314 ATFP-TTPGK-TAPEAEAFLASKGYLVRAVGNYNLPHAIRITIGLEEQNRAVVELLSQFM 371 Lambda K H 0.319 0.136 0.405 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: 385 Number of extensions: 18 Number of successful extensions: 3 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: 364 Length of database: 373 Length adjustment: 30 Effective length of query: 334 Effective length of database: 343 Effective search space: 114562 Effective search space used: 114562 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 CCNA_02306 CCNA_02306 (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.31552.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.3e-93 296.8 0.0 1e-92 296.6 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_02306 CCNA_02306 histidinol-phosphate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_02306 CCNA_02306 histidinol-phosphate aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 296.6 0.0 1e-92 1e-92 3 348 .. 19 369 .. 17 370 .. 0.95 Alignments for each domain: == domain 1 score: 296.6 bits; conditional E-value: 1e-92 TIGR01141 3 kikklepYqpgarel.gekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgveeen 74 i ++++Y+ g++++ g+ + vkL+snEn +g s+k+k+a+++++++lh Ypd +a l++a+a+++++e+e lcl|FitnessBrowser__Caulo:CCNA_02306 19 GIMDIHAYVGGKSKVeGIAHPVKLSSNENILGSSDKAKDAYRNAVDRLHIYPDGKANFLRAAVAERYKLEPER 91 6889999*99955551556****************************************************** PP TIGR01141 75 illgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklv 147 +++g+Gsde+ ll++ +lepgd++++ e+ ++ Y++ a++++ ev+ ++ ++ + d ++v + ++e+++lv lcl|FitnessBrowser__Caulo:CCNA_02306 92 LTFGDGSDEIFALLCQVYLEPGDNIVQGEHGFAAYAIGARACQGEVRMAKEVNH-RVDIDEVIKCVDERTRLV 163 ***********************************************9999888.688888888********* PP TIGR01141 148 flasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlvvlrTlSKafgLAg 216 f+a+P nPtG++l+ eei+++ ++ +++ V+D AY eF+++ ++ lel++ +n++v+rT+SK++gLA+ lcl|FitnessBrowser__Caulo:CCNA_02306 164 FIANPANPTGTWLTGEEIRALHAALpPSVVLVLDGAYAEFCSDphfEDGLELARTAENVIVTRTFSKIHGLAA 236 *************************66****************999999************************ PP TIGR01141 217 lRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSk 289 lRvG ++a ++ii +e++r+p+n+s +a+eaavaal d+d+ ++ + v++ r +l ++l l glev +S lcl|FitnessBrowser__Caulo:CCNA_02306 237 LRVGWGYAPEHIIAPIERIRPPFNTSIPAQEAAVAALFDDDFQDRSRALVEQWRPWLAQQLGGL-GLEVTPSA 308 ****************************************************************.8******* PP TIGR01141 290 aNFvlikvke....daeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348 aNFvl+ +++ +a e+ l kg++vR ++++ + l++++Rit+G +e+n++++e l++ lcl|FitnessBrowser__Caulo:CCNA_02306 309 ANFVLATFPTtpgkTAPEAEAFLASKGYLVRAVGNY-N-LPHAIRITIGLEEQNRAVVELLSQ 369 *********998877888888899************.5.6******************99976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (373 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: 9.20 // [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