Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate H281DRAFT_01942 H281DRAFT_01942 histidinol-phosphate aminotransferase
Query= reanno::Marino:GFF2483 (350 letters) >FitnessBrowser__Burk376:H281DRAFT_01942 Length = 359 Score = 417 bits (1072), Expect = e-121 Identities = 204/353 (57%), Positives = 263/353 (74%), Gaps = 3/353 (0%) Query: 1 MSKFWSPLVNDLVPYVPGEQPKMANLVKLNTNENPFGPSPKVIEAIQAELNDG---LRLY 57 +S++WS +V+ L PYVPGEQP +A VKLNTNENP+ PSP+V+EAI+ EL D LR Y Sbjct: 1 LSRYWSDIVHRLTPYVPGEQPLLARPVKLNTNENPYPPSPRVLEAIRQELGDAGESLRRY 60 Query: 58 PDPEGESLRETIAAYHKITPEQIFLGNGSDEVLAHIFFGLFQHGEPILFPDITYSFYPVY 117 PDP LRET+AAYH I +Q+F GNGSDEVLA F L +H +P+LFPDITYSFYP Y Sbjct: 61 PDPTAFKLRETVAAYHGIRADQVFAGNGSDEVLALTFQALLKHDKPLLFPDITYSFYPTY 120 Query: 118 CGLYNIESKKVPLTESFEINPEDFKQPNGGVIFPNPNAPTGRYLELQYVEEILAANPNRV 177 L+ ++ + +PL +SF IN +D+ NGG++FPNPNAPTGR L L +E ++ + + V Sbjct: 121 ARLFEVDYQTIPLDDSFAINVDDYAIANGGILFPNPNAPTGRPLPLADIERLVKKSADSV 180 Query: 178 VVVDEAYIDFGGESAITLVDKYPNLLVSQTLSKARSLAGLRVGFAVGHPDLIEALNRVKN 237 VV+DEAY+DFG ESAI L+D+YPNLLV QT+SK+RSLAG+RVGFA G+ +LI+ALNRVK+ Sbjct: 181 VVIDEAYVDFGAESAIGLIDRYPNLLVVQTVSKSRSLAGMRVGFAFGNAELIDALNRVKD 240 Query: 238 SFNSYPLDRLALAGAKAAYEDEAWFRKCCDGVISERERVTAVLEGLGFEVLPSKANFIFA 297 SFNSYPLDRLA A+AAYED+ WFR C VI+ RER++A L LGF+V+PS AN +FA Sbjct: 241 SFNSYPLDRLAQVAARAAYEDDRWFRDTCAKVIASRERLSAGLTALGFDVVPSAANLLFA 300 Query: 298 RHKEQPGEVLAKGLREQGIIVRHFNKPRISEFLRITIGTVEQNDALIARLESL 350 RH+ +L LRE+ I VRHFN PRI + LRI++GT + L+ L + Sbjct: 301 RHEAYDAAMLVSLLREREIFVRHFNAPRIDQHLRISVGTDAECGVLLDALRDI 353 Lambda K H 0.319 0.139 0.410 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: 448 Number of extensions: 17 Number of successful extensions: 2 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: 350 Length of database: 359 Length adjustment: 29 Effective length of query: 321 Effective length of database: 330 Effective search space: 105930 Effective search space used: 105930 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate H281DRAFT_01942 H281DRAFT_01942 (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.9535.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-93 299.6 0.0 1.5e-93 299.4 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_01942 H281DRAFT_01942 histidinol-phosp Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_01942 H281DRAFT_01942 histidinol-phosphate aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 299.4 0.0 1.5e-93 1.5e-93 4 349 .] 9 353 .. 6 353 .. 0.94 Alignments for each domain: == domain 1 score: 299.4 bits; conditional E-value: 1.5e-93 TIGR01141 4 ikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk....klhrYpdpqalelkeala 65 ++ l+pY+pg++ l vkLn+nEnP++ps++v+ea+++el +l+rYpdp a++l+e++a lcl|FitnessBrowser__Burk376:H281DRAFT_01942 9 VHRLTPYVPGEQPLLA-RPVKLNTNENPYPPSPRVLEAIRQELGdageSLRRYPDPTAFKLRETVA 73 7889*****9888777.5*************************888889***************** PP TIGR01141 66 kylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqe 131 +y g+ ++++++gnGsde++ l ++a+l+ + l+++ tys Y+++a++ +++++++pl++++ lcl|FitnessBrowser__Burk376:H281DRAFT_01942 74 AYHGIRADQVFAGNGSDEVLALTFQALLKHDKPLLFPDITYSFYPTYARLFEVDYQTIPLDDSFAI 139 ***************************************************************988 PP TIGR01141 132 dleavleaakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlella 197 ++++ + a + + + +Pn+PtG l ++ie+++++++d +VV+DeAY++F e s++ l+ lcl|FitnessBrowser__Burk376:H281DRAFT_01942 140 NVDDYAIA-NG---GILFPNPNAPTGRPLPLADIERLVKKSADSVVVIDEAYVDFGAE-SAIGLID 200 99888832.22...35679*********************99***************7.******* PP TIGR01141 198 eypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapyn...vsslaleaavaalrdsdkie 260 +ypnl+v++T+SK+ +LAg+RvG+a++nae+i+al++v++++n +++la+ aa aa++d++ ++ lcl|FitnessBrowser__Burk376:H281DRAFT_01942 201 RYPNLLVVQTVSKSRSLAGMRVGFAFGNAELIDALNRVKDSFNsypLDRLAQVAARAAYEDDRWFR 266 ***************************************87543339******************* PP TIGR01141 261 ktveevkkererlleelkkleglevyeSkaNFvlikvke.daeelleallekgiivRdlksaegll 325 +t ++v+++rerl ++l++l g++v++S aN ++++ ++ da+ l+ l e++i vR++++ + lcl|FitnessBrowser__Burk376:H281DRAFT_01942 267 DTCAKVIASRERLSAGLTAL-GFDVVPSAANLLFARHEAyDAAMLVSLLREREIFVRHFNAP--RI 329 ********************.8**************99999******************944..68 PP TIGR01141 326 eeclRitvGtreenerllealkei 349 +++lRi+vGt+ e+ ll+al++i lcl|FitnessBrowser__Burk376:H281DRAFT_01942 330 DQHLRISVGTDAECGVLLDALRDI 353 ********************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (359 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: 10.57 // [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