Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate PfGW456L13_4999 Histidinol-phosphate aminotransferase (EC 2.6.1.9)
Query= reanno::pseudo6_N2E2:Pf6N2E2_3251 (350 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999 Length = 350 Score = 665 bits (1716), Expect = 0.0 Identities = 328/350 (93%), Positives = 343/350 (98%) Query: 1 MSKFWSPFVKNLVPYVPGEQPKLTRLVKLNTNENPYGPSPKALAAMQTELNDNLRLYPDP 60 MSKFWSPFVKNLVPYVPGEQPKL +LVKLNTNENPYGPSPKALAAMQTELNDNLRLYPDP Sbjct: 1 MSKFWSPFVKNLVPYVPGEQPKLAKLVKLNTNENPYGPSPKALAAMQTELNDNLRLYPDP 60 Query: 61 NSDLLKGAVARYYGVQSNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGL 120 NSDLLK AVARYYGVQSNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGL Sbjct: 61 NSDLLKNAVARYYGVQSNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGL 120 Query: 121 YGIQFDAVPLDAQFQIDPADYAKPNGGIIFPNPNAPTGCLLALEAVEQILKANPDSVVVV 180 YGI+FDAVPLD QFQI+PADYA+PNGGIIFPNPNAPTGCLLALEAVEQILKA+PDSVVVV Sbjct: 121 YGIKFDAVPLDEQFQINPADYARPNGGIIFPNPNAPTGCLLALEAVEQILKASPDSVVVV 180 Query: 181 DEAYIDFGGETAISLVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPELIEALERIKNSFN 240 DEAYIDFGGETAI+LVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHP+LIEALERIKNSFN Sbjct: 181 DEAYIDFGGETAITLVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPDLIEALERIKNSFN 240 Query: 241 SYPLDRLANVGGAAAFDDREYFDRTCRLVIEHREWVVAQLQAKGFEVLPSAANFIFARHP 300 SYPLDR+ANVG AAAF+DREYFD+TCRLVIE+RE VVAQL+ KGFEVLPSAANFIFARHP Sbjct: 241 SYPLDRMANVGAAAAFEDREYFDKTCRLVIENREKVVAQLEEKGFEVLPSAANFIFARHP 300 Query: 301 RHDAAGLAAKLREQGVIVRHFKQERIAQFLRISIGTPEQNQALIEALGEL 350 R+DAAGLAAKLREQGVIVRHFKQERIAQFLRISIGTPEQNQALI+ LG+L Sbjct: 301 RYDAAGLAAKLREQGVIVRHFKQERIAQFLRISIGTPEQNQALIDGLGDL 350 Lambda K H 0.320 0.139 0.413 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: 614 Number of extensions: 12 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: 350 Length of database: 350 Length adjustment: 29 Effective length of query: 321 Effective length of database: 321 Effective search space: 103041 Effective search space used: 103041 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 PfGW456L13_4999 (Histidinol-phosphate aminotransferase (EC 2.6.1.9))
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.2971978.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-96 307.9 0.0 4.3e-96 307.8 0.0 1.0 1 FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999 Domain annotation for each sequence (and alignments): >> FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 307.8 0.0 4.3e-96 4.3e-96 3 347 .. 8 348 .. 6 350 .] 0.94 Alignments for each domain: == domain 1 score: 307.8 bits; conditional E-value: 4.3e-96 TIGR01141 3 kikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk.klhrYpdpqalel 60 +k+l pY+pg++ + + vkLn+nEnP+gps+k+++a++ el+ +l++Ypdp++ l FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999 8 FVKNLVPYVPGEQPKLA-KLVKLNTNENPYGPSPKALAAMQTELNdNLRLYPDPNSDLL 65 699*******9777766.5*************************99************* PP TIGR01141 61 kealakylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagae 119 k+a+a+y+gv+ ++++lgnGsde++ +++ +l+ + l+++ +ys Y+v+ ++g++ FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999 66 KNAVARYYGVQSNQVFLGNGSDEVLAHIFHGLLQHDQPLLFPDISYSFYPVYCGLYGIK 124 *********************************************************** PP TIGR01141 120 vkevplkedgqedleavleaakekvklvflasPnnPtGnllkreeiekvleevedalVV 178 vpl+e++q + ++ + + + + +Pn+PtG ll e +e++l+++ d +VV FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999 125 FDAVPLDEQFQINPADYA---RPNGG-IIFPNPNAPTGCLLALEAVEQILKASPDSVVV 179 *********988888877...44444.5558*********************98***** PP TIGR01141 179 vDeAYieFseeasvlellaeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvra 237 vDeAYi+F +e +++ l+ +ypnl+v++TlSK+ +LAglRvG+a++++++ieale++++ FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999 180 VDEAYIDFGGE-TAITLVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPDLIEALERIKN 237 **********7.**********************************************8 PP TIGR01141 238 pyn...vsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSkaNFv 293 ++n ++++a a aa +d++++ kt + v+++re + ++l++ g+ev +S aNF+ FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999 238 SFNsypLDRMANVGAAAAFEDREYFDKTCRLVIENREKVVAQLEEK-GFEVLPSAANFI 295 75433399************************************99.8*********** PP TIGR01141 294 likvke.daeelleallekgiivRdlksaeglleeclRitvGtreenerllealk 347 +++ ++ da+ l+ +l e+g+ivR++k+ + ++lRi++Gt+e+n++l++ l FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4999 296 FARHPRyDAAGLAAKLREQGVIVRHFKQE--RIAQFLRISIGTPEQNQALIDGLG 348 *****99*******************977..48*****************98775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (350 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 27.35 // [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