Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate WP_090447996.1 BLS63_RS22285 histidinol-phosphate transaminase
Query= reanno::psRCH2:GFF3234 (348 letters) >NCBI__GCF_900100495.1:WP_090447996.1 Length = 350 Score = 613 bits (1582), Expect = e-180 Identities = 304/347 (87%), Positives = 323/347 (93%) Query: 1 MSKFWSPFVKDLVPYVPGEQPKLSKLVKLNTNENPYGPSPRAIAAMQAELNDSLRLYPDP 60 MSKFWSPFVKDLVPYVPGEQPKL+KLVKLNTNENPYGPSP+AIAAMQAEL D+LRLYPDP Sbjct: 1 MSKFWSPFVKDLVPYVPGEQPKLAKLVKLNTNENPYGPSPKAIAAMQAELGDNLRLYPDP 60 Query: 61 NGERLKQAVADYYGVQPAQVFVGNGSDEVLAHAFHGLFQHAGPLLFPDISYSFYPVYCGL 120 NGERLKQAVADYYGV PAQVFVGNGSDEVLAHAFHGLFQH PLLFPDISYSFYPVYCGL Sbjct: 61 NGERLKQAVADYYGVTPAQVFVGNGSDEVLAHAFHGLFQHGRPLLFPDISYSFYPVYCGL 120 Query: 121 YGIAYETVALDEQFQIDVADYNRPNGGIIFPNPNAPTGCLLALEAIERLLQANTETVVLV 180 YGI +E VALDEQFQI V DY RPNGGI+FPNPNAPTGCLL L AIERLL+AN ++VVLV Sbjct: 121 YGIPFEAVALDEQFQIRVEDYARPNGGIVFPNPNAPTGCLLPLTAIERLLEANPDSVVLV 180 Query: 181 DEAYVDFGGESAIALVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPDLIEALERIKNSFN 240 DEAYVDFGGE+AI+LVD+YPNLLVTQTLSKSRSLAGLRVGLAVGHP+LIEALERIKNSFN Sbjct: 181 DEAYVDFGGETAISLVDKYPNLLVTQTLSKSRSLAGLRVGLAVGHPELIEALERIKNSFN 240 Query: 241 SYPLDRIAIAGAAAAFEDRAYFQQTCQQVIDSREAVVAAMQGLGFEVLPSAANFIFARHP 300 SYPLDR+AIAGAAAAF DR YF +TCQ VI SREAVVA +Q LGFEVLPSAANF+FARHP Sbjct: 241 SYPLDRLAIAGAAAAFADREYFAKTCQAVIASREAVVAGLQQLGFEVLPSAANFVFARHP 300 Query: 301 QRDAATIAASLREQGVIVRHFKQRRIEQFLRITIGTPEQNQALLEAL 347 QRDAA +AA LREQGVIVRHFKQ RI QFLRI+IG PEQNQALL+AL Sbjct: 301 QRDAAELAAQLREQGVIVRHFKQARIAQFLRISIGAPEQNQALLDAL 347 Lambda K H 0.320 0.137 0.401 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: 566 Number of extensions: 14 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: 348 Length of database: 350 Length adjustment: 29 Effective length of query: 319 Effective length of database: 321 Effective search space: 102399 Effective search space used: 102399 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 WP_090447996.1 BLS63_RS22285 (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.10044.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-97 310.3 0.0 7.9e-97 310.2 0.0 1.0 1 lcl|NCBI__GCF_900100495.1:WP_090447996.1 BLS63_RS22285 histidinol-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_090447996.1 BLS63_RS22285 histidinol-phosphate transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 310.2 0.0 7.9e-97 7.9e-97 3 347 .. 8 348 .. 6 350 .] 0.95 Alignments for each domain: == domain 1 score: 310.2 bits; conditional E-value: 7.9e-97 TIGR01141 3 kikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk.klhrYpdpqalelkealakylgv 70 +k+l pY+pg++ + + vkLn+nEnP+gps+k+++a+++el +l++Ypdp++ +lk+a+a+y+gv lcl|NCBI__GCF_900100495.1:WP_090447996.1 8 FVKDLVPYVPGEQPKLA-KLVKLNTNENPYGPSPKAIAAMQAELGdNLRLYPDPNGERLKQAVADYYGV 75 699*******9777766.5*************************88*********************** PP TIGR01141 71 eeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavlea 139 +++++++gnGsde++ ++ + + g+ l+++ +ys Y+v+ ++g+ v+l+e++q +e+ + lcl|NCBI__GCF_900100495.1:WP_090447996.1 76 TPAQVFVGNGSDEVLAHAFHGLFQHGRPLLFPDISYSFYPVYCGLYGIPFEAVALDEQFQIRVEDYA-- 142 **********************************************************988888877.. PP TIGR01141 140 akekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTl 208 + +vf +Pn+PtG ll ie++le+ d +V+vDeAY++F +e ++++l+ +ypnl+v++Tl lcl|NCBI__GCF_900100495.1:WP_090447996.1 143 -RPNGGIVF-PNPNAPTGCLLPLTAIERLLEANPDSVVLVDEAYVDFGGE-TAISLVDKYPNLLVTQTL 208 .66666776.89********************77***************7.****************** PP TIGR01141 209 SKafgLAglRvGyaianaeiiealekvrapyn...vsslaleaavaalrdsdkiektveevkkererll 274 SK+ +LAglRvG+a++++e+ieale++++++n +++la + a aa d+++++kt ++v+++re + lcl|NCBI__GCF_900100495.1:WP_090447996.1 209 SKSRSLAGLRVGLAVGHPELIEALERIKNSFNsypLDRLAIAGAAAAFADREYFAKTCQAVIASREAVV 277 ****************************87543339********************************* PP TIGR01141 275 eelkkleglevyeSkaNFvlikvke.daeelleallekgiivRdlksaeglleeclRitvGtreenerl 342 ++l++l g+ev +S aNFv+++ ++ da+el+ +l e+g+ivR++k+a + ++lRi++G +e+n++l lcl|NCBI__GCF_900100495.1:WP_090447996.1 278 AGLQQL-GFEVLPSAANFVFARHPQrDAAELAAQLREQGVIVRHFKQA--RIAQFLRISIGAPEQNQAL 343 ******.8***************999********************88..489**************** PP TIGR01141 343 lealk 347 l+al+ lcl|NCBI__GCF_900100495.1:WP_090447996.1 344 LDALQ 348 **997 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.06 // [ok]
This GapMind analysis is from Apr 10 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