Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_085217034.1 B9N75_RS00545 histidinol-phosphate transaminase
Query= curated2:P58891 (363 letters) >NCBI__GCF_900177405.1:WP_085217034.1 Length = 549 Score = 212 bits (540), Expect = 2e-59 Identities = 141/334 (42%), Positives = 191/334 (57%), Gaps = 12/334 (3%) Query: 27 ALQGD-VWLNANESAWA--NPADPDASTRRYPDPQPKGLRSALAALYGCAPEQLLIGRGS 83 A+ GD + L+ANE+ + PA AS RYP+PQP L++ LA+LYG P+ L++ RG+ Sbjct: 25 AVPGDTIKLDANENPFEPLGPAALAASVNRYPEPQPARLKAMLASLYGVDPDALVVTRGA 84 Query: 84 DEAIDLLVRGLCVPERDAVLVTPPVFGMYAVCARLQNAPLVDVPLVDGPDGFHADIPAIV 143 D+AID+L+R C P DA+L+ PP F YA ARLQ A +V+ L GPD F D V Sbjct: 85 DDAIDMLIRAFCRPGDDAILIAPPTFTAYAHFARLQGARVVEHYL--GPD-FALDAQGFV 141 Query: 144 AMALSS-NAKLVFLCSPSNPAGSAIALDQIEQALQALQGKALVVVDEAYGEFSDVPSAVG 202 A A ++ + KL FLCSP NP G +A D + AL + ++VVDEAY EFS S Sbjct: 142 AAARATPSLKLAFLCSPDNPTGGIVAADTLCAIADALP-ETILVVDEAYIEFSCAESVAR 200 Query: 203 LLGRYDNLAVLRTLSKAHALAAARIGTLIANAELIALLRRCQAPYPVPTPCAAMAEQALS 262 R NL VLRTLSKA LA ARIG I + LIAL R PYP+ + A A AL+ Sbjct: 201 EAVRRPNLVVLRTLSKAFGLAGARIGAAIGSRALIALAARALPPYPLSSLSIAAALDALA 260 Query: 263 APALEVTRRRIAEVRSERERMHKALVQLPGVRQVYPSQGNFLLVRFDDAEGAFQALLEAG 322 + RIA + +ER RM + L + G+ +V GNFL + D ++ AG Sbjct: 261 PERRRLHADRIARIIAERARMAERLRRASGLDRVRDGGGNFLFLEAKDPAKLRESFAAAG 320 Query: 323 VVVR-DQRAVPRLADALRITLGTNEQNQRVLSAL 355 ++ R + A P +R+T+GT +N VL+AL Sbjct: 321 ILARFRETAAP---GGVRLTIGTRAENDAVLAAL 351 Lambda K H 0.319 0.133 0.382 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: 530 Number of extensions: 35 Number of successful extensions: 4 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: 363 Length of database: 549 Length adjustment: 32 Effective length of query: 331 Effective length of database: 517 Effective search space: 171127 Effective search space used: 171127 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: 51 (24.3 bits)
Align candidate WP_085217034.1 B9N75_RS00545 (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.1268802.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-91 290.6 0.0 8.8e-91 290.3 0.0 1.1 1 NCBI__GCF_900177405.1:WP_085217034.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900177405.1:WP_085217034.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 290.3 0.0 8.8e-91 8.8e-91 2 346 .. 11 351 .. 10 353 .. 0.94 Alignments for each domain: == domain 1 score: 290.3 bits; conditional E-value: 8.8e-91 TIGR01141 2 ekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgveeen 74 ++i +l ++++ r+++++ ++kL++nEnPf+p a+ ++ +++rYp+pq+++lk++la+ +gv+++ NCBI__GCF_900177405.1:WP_085217034.1 11 PEIVALGDFDIPPRAVPGD-TIKLDANENPFEPLG---PAALAA--SVNRYPEPQPARLKAMLASLYGVDPDA 77 6677777777777888885.9************95...444444..7************************** PP TIGR01141 75 illgnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedleavle..aakekv 144 +++++G+d++i++liraf+ pg da+l+++pt++ Y++ a+++ga+v+e l d+ d + + + a+ + NCBI__GCF_900177405.1:WP_085217034.1 78 LVVTRGADDAIDMLIRAFCRPGdDAILIAPPTFTAYAHFARLQGARVVEHYLGPDFALDAQGFVAaaRATPSL 150 **********************99*******************************999999988744667788 PP TIGR01141 145 klvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLAgl 217 kl fl+sP+nPtG ++ ++ +++++++ +++ VvDeAYieFs +sv+ + ++pnlvvlrTlSKafgLAg NCBI__GCF_900177405.1:WP_085217034.1 151 KLAFLCSPDNPTGGIVAADTLCAIADALPETILVVDEAYIEFSCAESVAREAVRRPNLVVLRTLSKAFGLAGA 223 9**************************989******************************************* PP TIGR01141 218 RvGyaianaeiiealekvrapynvsslaleaavaalrdsd..kiektveevkkererlleelkklegle.vye 287 R+G ai++ ++i ++ +py++ssl+ +aa+ al ++ +++++++++er+r+ e l+ +gl+ v + NCBI__GCF_900177405.1:WP_085217034.1 224 RIGAAIGSRALIALAARALPPYPLSSLSIAAALDALAPERrrLHADRIARIIAERARMAERLRRASGLDrVRD 296 ************************************9998878899***********************9*** PP TIGR01141 288 SkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerlleal 346 + +NF+++++k d ++l e+ +gi+ R ++a ++ +R+t+Gtr en+++l+al NCBI__GCF_900177405.1:WP_085217034.1 297 GGGNFLFLEAK-DPAKLRESFAAAGILARFRETA---APGGVRLTIGTRAENDAVLAAL 351 *********99.999****************966...599****************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (549 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: 00:00:00.00 # Mc/sec: 20.81 // [ok]
This GapMind analysis is from Jul 26 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