Align Histidinol-phosphate aminotransferase 1; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 1 (uncharacterized)
to candidate WP_013012192.1 DACET_RS14925 histidinol-phosphate transaminase
Query= curated2:Q3JEN8 (370 letters) >NCBI__GCF_000025725.1:WP_013012192.1 Length = 363 Score = 310 bits (793), Expect = 5e-89 Identities = 163/362 (45%), Positives = 233/362 (64%), Gaps = 3/362 (0%) Query: 6 FYQLAAAGVQGLTPYQPGKPIEELEREYGVRGAVKLASNENPLGPSPMAIDAIYGVLGES 65 + +LA + LTPY+PGKP++ELERE GV +VKLASNENPLG SP I A+ + E Sbjct: 4 YSKLAGQSISALTPYKPGKPVKELERELGVTNSVKLASNENPLGCSPKVIAALNEFMPEI 63 Query: 66 GRYPDGNGFALKTALSQCLGIPANQITLGNGSSDLLEFAARVLISPEHEVIYSQYCFALY 125 RYP G+ F L+ A+S+ GI +++ G GS++++E A R ++ + V+ F++Y Sbjct: 64 SRYPLGDAFYLRKAVSEHYGISGDRLLFGTGSNEIIELAIRTFLAEDECVLSPSPSFSVY 123 Query: 126 PLLIQILGAKGHAVPAK-GFGHDLEAMVKAVNSQTRLVYIANPNNPTGTWLHSDELEAFL 184 ++ Q G VP F D EA+ A+ +TR+V++ANPNNPTG + ++ELEAF+ Sbjct: 124 GIISQAAGKSCKWVPVNDAFKCDFEALANAITDKTRMVFLANPNNPTGEYFTAEELEAFM 183 Query: 185 AALPEHVLVVLDEAYYEYVNEAQYPYSLAWMSRYPNLMITRTFSKIYGLAGLRIGYGVSH 244 +PE V+VV+DEAY EY + +P +L + +Y N+ + RTFSK YGLA LR G+ ++ Sbjct: 184 QKVPEDVIVVMDEAYIEYADAPDFPDTLKMLDKYKNMFLMRTFSKAYGLAALRAGFVIAC 243 Query: 245 PDLADLMNRVRPPFNVNSLALAAATAALQDHDHLQRSRKVNQAGMAQLTMAFTALGLDYI 304 + D+MNRVR PFN N A AA AA++D HL+ NQ G L F LGL Y+ Sbjct: 244 EEAIDMMNRVRQPFNTNMAAQVAAEAAIKDQTHLKAVLAENQRGKEFLYSEFEKLGLKYV 303 Query: 305 PSVANFVTVDVKQSGDKVYENLLRHGVIVRPMTGYGLPRHVRVTVGREEENARFIQVLET 364 P+ ANF+ V+V +G+KV++NLL+ GVIVR G GL +RV++G EENA FI+ L+ Sbjct: 304 PTQANFILVNV-GNGEKVFDNLLKQGVIVR-FFGSGLAEWIRVSIGTMEENAIFIEKLKE 361 Query: 365 VL 366 VL Sbjct: 362 VL 363 Lambda K H 0.319 0.136 0.400 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: 341 Number of extensions: 11 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: 370 Length of database: 363 Length adjustment: 30 Effective length of query: 340 Effective length of database: 333 Effective search space: 113220 Effective search space used: 113220 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_013012192.1 DACET_RS14925 (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.19185.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-111 356.9 0.0 5.5e-111 356.8 0.0 1.0 1 lcl|NCBI__GCF_000025725.1:WP_013012192.1 DACET_RS14925 histidinol-phospha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025725.1:WP_013012192.1 DACET_RS14925 histidinol-phosphate transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 356.8 0.0 5.5e-111 5.5e-111 2 349 .] 10 362 .. 9 362 .. 0.98 Alignments for each domain: == domain 1 score: 356.8 bits; conditional E-value: 5.5e-111 TIGR01141 2 ekikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkeal 64 ++i++l+pY+pg +relg ++ vkL+snEnP+g+s+kv++al+e + ++ rYp +a+ l++a+ lcl|NCBI__GCF_000025725.1:WP_013012192.1 10 QSISALTPYKPGkpvkelERELGVTNSVKLASNENPLGCSPKVIAALNEFMPEISRYPLGDAFYLRKAV 78 6899***************************************************************** PP TIGR01141 65 akylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedl 133 ++++g++ + +l+g Gs+e+iel ir+fl + + vl ++p++s+Y +++++ag ++k vp+++ ++ d+ lcl|NCBI__GCF_000025725.1:WP_013012192.1 79 SEHYGISGDRLLFGTGSNEIIELAIRTFLAEDECVLSPSPSFSVYGIISQAAGKSCKWVPVNDAFKCDF 147 ********************************************************************* PP TIGR01141 134 eavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellae 198 ea+++a+++k+++vfla+PnnPtG+++++ee+e+++++v ed++VV+DeAYie+++ +++l++l + lcl|NCBI__GCF_000025725.1:WP_013012192.1 148 EALANAITDKTRMVFLANPNNPTGEYFTAEELEAFMQKVpEDVIVVMDEAYIEYADApdfPDTLKMLDK 216 ***************************************99***************999999******* PP TIGR01141 199 ypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevk 267 y n++ +rT+SKa+gLA+lR G++ia++e i+++++vr+p+n++ a+ aa aa++d+ +++++++e++ lcl|NCBI__GCF_000025725.1:WP_013012192.1 217 YKNMFLMRTFSKAYGLAALRAGFVIACEEAIDMMNRVRQPFNTNMAAQVAAEAAIKDQTHLKAVLAENQ 285 ********************************************************************* PP TIGR01141 268 kererlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtr 336 +++e l++e++kl gl++++ +aNF+l++v + e+++++ll++g+ivR ++ +g l e++R+++Gt lcl|NCBI__GCF_000025725.1:WP_013012192.1 286 RGKEFLYSEFEKL-GLKYVPTQANFILVNVG-NGEKVFDNLLKQGVIVRFFG--SG-LAEWIRVSIGTM 349 *************.8***************9.*******************9..46.59********** PP TIGR01141 337 eenerllealkei 349 een ++e lke+ lcl|NCBI__GCF_000025725.1:WP_013012192.1 350 EENAIFIEKLKEV 362 **********986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (363 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: 11.41 // [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