Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate WP_011767071.1 AZO_RS16805 histidinol-phosphate transaminase
Query= reanno::psRCH2:GFF3234 (348 letters) >NCBI__GCF_000061505.1:WP_011767071.1 Length = 362 Score = 468 bits (1203), Expect = e-136 Identities = 235/351 (66%), Positives = 274/351 (78%), Gaps = 4/351 (1%) Query: 1 MSKFWSPFVKDLVPYVPGEQPKLSKLVKLNTNENPYGPSPRAIAAMQAELNDSLRLYPDP 60 MS++WS V L PYVPGEQPKL LVKLNTNE+PYGPSPRA+ A++A +D+LRLYPDP Sbjct: 1 MSRYWSAVVHGLTPYVPGEQPKLDNLVKLNTNEHPYGPSPRALEAIRAATSDALRLYPDP 60 Query: 61 NGERLKQAVADYYGVQPAQVFVGNGSDEVLAHAFHGLFQHAGPLLFPDISYSFYPVYCGL 120 N + LKQA+A Y V+ AQ+FVGNGSDEVLAHAF L +H PL FPDISYSFYPVYCGL Sbjct: 61 NADALKQALAARYRVKAAQIFVGNGSDEVLAHAFMALLRHERPLWFPDISYSFYPVYCGL 120 Query: 121 YGIAYETVALDEQFQIDVADY----NRPNGGIIFPNPNAPTGCLLALEAIERLLQANTET 176 YG+ V LD F I DY G IIFPNPNAPTG LL L IER++ N + Sbjct: 121 YGVPSRVVPLDADFAIRADDYLPRGEDRAGAIIFPNPNAPTGRLLPLADIERIVAGNPDA 180 Query: 177 VVLVDEAYVDFGGESAIALVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPDLIEALERIK 236 VVLVDEAYVDFGGESAIALVDR+PNLLV QT SKSRSLAGLRVG AVGHP LIEALER+K Sbjct: 181 VVLVDEAYVDFGGESAIALVDRHPNLLVVQTFSKSRSLAGLRVGFAVGHPALIEALERVK 240 Query: 237 NSFNSYPLDRIAIAGAAAAFEDRAYFQQTCQQVIDSREAVVAAMQGLGFEVLPSAANFIF 296 NSFNSYPLDR+AIAGA A+ ED A+F +C +VI +RE + AA+ LGF+VLPSAANF+F Sbjct: 241 NSFNSYPLDRLAIAGAVASVEDEAHFSDSCAKVIATRERLTAALAALGFQVLPSAANFVF 300 Query: 297 ARHPQRDAATIAASLREQGVIVRHFKQRRIEQFLRITIGTPEQNQALLEAL 347 ARHP DA ++A+LRE+ +IVRHF+Q RI+QFLRIT+GT Q + L+ L Sbjct: 301 ARHPAHDAGQLSAALRERAIIVRHFRQPRIDQFLRITVGTDAQCETLVAGL 351 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: 497 Number of extensions: 20 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: 362 Length adjustment: 29 Effective length of query: 319 Effective length of database: 333 Effective search space: 106227 Effective search space used: 106227 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_011767071.1 AZO_RS16805 (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.27828.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-95 303.9 0.0 7.2e-95 303.7 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011767071.1 AZO_RS16805 histidinol-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000061505.1:WP_011767071.1 AZO_RS16805 histidinol-phosphate transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 303.7 0.0 7.2e-95 7.2e-95 4 349 .] 9 354 .. 6 354 .. 0.96 Alignments for each domain: == domain 1 score: 303.7 bits; conditional E-value: 7.2e-95 TIGR01141 4 ikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk.klhrYpdpqalelkealakylgve 71 ++ l+pY+pg++ + + + vkLn+nE+P+gps++++ea++++ + l++Ypdp+a +lk+ala+++ v+ lcl|NCBI__GCF_000061505.1:WP_011767071.1 9 VHGLTPYVPGEQPKLD-NLVKLNTNEHPYGPSPRALEAIRAATSdALRLYPDPNADALKQALAARYRVK 76 7889*****9666665.6**********************998889*********************** PP TIGR01141 72 eenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaa 140 +++i++gnGsde++ ++a+l ++ +++ +ys Y+v+ ++g+ + vpl++d+ ++ l lcl|NCBI__GCF_000061505.1:WP_011767071.1 77 AAQIFVGNGSDEVLAHAFMALLRHERPLWFPDISYSFYPVYCGLYGVPSRVVPLDADFAIRADDYLPRG 145 *********************************************************999********* PP TIGR01141 141 kekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlS 209 ++++ + + +Pn+PtG ll ++ie++++ da+V+vDeAY++F +e s++ l+ ++pnl+v++T+S lcl|NCBI__GCF_000061505.1:WP_011767071.1 146 EDRAGAIIFPNPNAPTGRLLPLADIERIVAGNPDAVVLVDEAYVDFGGE-SAIALVDRHPNLLVVQTFS 213 *******************************77***************7.******************* PP TIGR01141 210 KafgLAglRvGyaianaeiiealekvrapyn...vsslaleaavaalrdsdkiektveevkkererlle 275 K+ +LAglRvG+a++++++ieale+v++++n +++la + ava+++d+++++++ ++v+++rerl++ lcl|NCBI__GCF_000061505.1:WP_011767071.1 214 KSRSLAGLRVGFAVGHPALIEALERVKNSFNsypLDRLAIAGAVASVEDEAHFSDSCAKVIATRERLTA 282 ***************************87543339********************************** PP TIGR01141 276 elkkleglevyeSkaNFvlikvke.daeelleallekgiivRdlksaeglleeclRitvGtreenerll 343 +l++l g++v +S aNFv+++ ++ da +l+ al e+ iivR++++ + ++++lRitvGt+ ++e l+ lcl|NCBI__GCF_000061505.1:WP_011767071.1 283 ALAAL-GFQVLPSAANFVFARHPAhDAGQLSAALRERAIIVRHFRQ--PRIDQFLRITVGTDAQCETLV 348 *****.8***************999*******************94..468****************** PP TIGR01141 344 ealkei 349 + l+ei lcl|NCBI__GCF_000061505.1:WP_011767071.1 349 AGLREI 354 999986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (362 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.21 // [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