Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate WP_086508681.1 BZY95_RS03940 histidinol-phosphate transaminase
Query= reanno::psRCH2:GFF3234 (348 letters) >NCBI__GCF_002151265.1:WP_086508681.1 Length = 351 Score = 385 bits (989), Expect = e-112 Identities = 195/346 (56%), Positives = 250/346 (72%), Gaps = 1/346 (0%) Query: 1 MSKFWSPFVKDLVPYVPGEQPKLSKLVKLNTNENPYGPSPRAIAAMQAELNDSLRLYPDP 60 MS+FWSP V++L PYVPGEQP+ KL+KLNTNENPY P+P AA++ D LRLYPDP Sbjct: 1 MSQFWSPAVRELTPYVPGEQPR-EKLIKLNTNENPYPPAPGVEAALREYPVDHLRLYPDP 59 Query: 61 NGERLKQAVADYYGVQPAQVFVGNGSDEVLAHAFHGLFQHAGPLLFPDISYSFYPVYCGL 120 L+QA+A +GV QVFVGNGSDEVLA AF F H PL PDI+YSFYPVYC L Sbjct: 60 QSLALRQALAREHGVAVEQVFVGNGSDEVLALAFQAFFCHERPLEMPDITYSFYPVYCKL 119 Query: 121 YGIAYETVALDEQFQIDVADYNRPNGGIIFPNPNAPTGCLLALEAIERLLQANTETVVLV 180 YGI ++ LD+++++D+ + +GG IF NPNAPT +AI LL+ T+ VVLV Sbjct: 120 YGIERRSLPLDDRWRVDLDAFTADSGGAIFANPNAPTAHGHPRDAIAGLLERLTDQVVLV 179 Query: 181 DEAYVDFGGESAIALVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPDLIEALERIKNSFN 240 DEAYVDFGGES + L++R+PNLLVT T SKSRSLAGLR+G A+G +LIE L R+K+SFN Sbjct: 180 DEAYVDFGGESVVPLIERFPNLLVTGTFSKSRSLAGLRLGYAIGSSELIEGLVRVKDSFN 239 Query: 241 SYPLDRIAIAGAAAAFEDRAYFQQTCQQVIDSREAVVAAMQGLGFEVLPSAANFIFARHP 300 SYP+D +A A A A+ EDR +F ++V+ +RE V + LGFEVLPS ANF+ ARHP Sbjct: 240 SYPIDSLASALAIASLEDREHFDACRERVVTTRERTVRRLGELGFEVLPSQANFVLARHP 299 Query: 301 QRDAATIAASLREQGVIVRHFKQRRIEQFLRITIGTPEQNQALLEA 346 + DAA + LRE+G++VRHF + FLRI+IGT ++ +L+EA Sbjct: 300 EHDAAQLFVGLRERGILVRHFNTEALRDFLRISIGTDDEMDSLIEA 345 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: 430 Number of extensions: 16 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: 348 Length of database: 351 Length adjustment: 29 Effective length of query: 319 Effective length of database: 322 Effective search space: 102718 Effective search space used: 102718 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_086508681.1 BZY95_RS03940 (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.31002.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-93 299.8 0.0 1.3e-93 299.6 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508681.1 BZY95_RS03940 histidinol-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508681.1 BZY95_RS03940 histidinol-phosphate transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 299.6 0.0 1.3e-93 1.3e-93 3 347 .. 8 347 .. 6 349 .. 0.95 Alignments for each domain: == domain 1 score: 299.6 bits; conditional E-value: 1.3e-93 TIGR01141 3 kikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkee.lkklhrYpdpqalelkealakylgv 70 +++l+pY+pg e+++++ +kLn+nEnP++p + v +al+e +++l++Ypdpq+l+l++ala++ gv lcl|NCBI__GCF_002151265.1:WP_086508681.1 8 AVRELTPYVPG--EQPREKLIKLNTNENPYPPAPGVEAALREYpVDHLRLYPDPQSLALRQALAREHGV 74 799*******9..888999*********************997477*********************** PP TIGR01141 71 eeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavlea 139 +e++++gnGsde++ l ++af ++ +++ tys Y+v+ k++g+e ++ pl++ ++ dl+a+ lcl|NCBI__GCF_002151265.1:WP_086508681.1 75 AVEQVFVGNGSDEVLALAFQAFFCHERPLEMPDITYSFYPVYCKLYGIERRSLPLDDRWRVDLDAFT-- 141 ***********************************************************99999999.. PP TIGR01141 140 akekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTl 208 +++ +a+Pn+Pt + r+ i +le+ +d +V+vDeAY++F +e sv++l++++pnl+v+ T+ lcl|NCBI__GCF_002151265.1:WP_086508681.1 142 -ADSGGA-IFANPNAPTAHGHPRDAIAGLLERLTDQVVLVDEAYVDFGGE-SVVPLIERFPNLLVTGTF 207 .333333.469*********************99***************7.****************** PP TIGR01141 209 SKafgLAglRvGyaianaeiiealekvrapyn...vsslaleaavaalrdsdkiektveevkkererll 274 SK+ +LAglR+Gyai++ e+ie l +v++++n ++sla+++a+a+l+d++++ ++ e+v +rer+ lcl|NCBI__GCF_002151265.1:WP_086508681.1 208 SKSRSLAGLRLGYAIGSSELIEGLVRVKDSFNsypIDSLASALAIASLEDREHFDACRERVVTTRERTV 276 ****************************87543339********************************* PP TIGR01141 275 eelkkleglevyeSkaNFvlikvke.daeelleallekgiivRdlksaeglleeclRitvGtreenerl 342 l +l g+ev +S+aNFvl++ +e da++l+ l e+gi+vR++++ l ++lRi++Gt++e++ l lcl|NCBI__GCF_002151265.1:WP_086508681.1 277 RRLGEL-GFEVLPSQANFVLARHPEhDAAQLFVGLRERGILVRHFNTE--ALRDFLRISIGTDDEMDSL 342 ******.8****************99*******************966..47***************** PP TIGR01141 343 lealk 347 +ea++ lcl|NCBI__GCF_002151265.1:WP_086508681.1 343 IEAFE 347 **986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (351 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: 10.43 // [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