Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_017550016.1 C792_RS0113615 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= reanno::psRCH2:GFF155 (247 letters) >NCBI__GCF_000330705.1:WP_017550016.1 Length = 233 Score = 163 bits (412), Expect = 3e-45 Identities = 94/228 (41%), Positives = 131/228 (57%), Gaps = 9/228 (3%) Query: 1 MLIIPAIDLKDGACVRLRQGLMDDATVFSDDP---VAMAAKWVEAGCRRLHLVDLNGAFE 57 M IIPAID+ DG VRL+QG D T P + + + + G R+H+VDL GA + Sbjct: 1 MNIIPAIDIIDGRNVRLKQGDYDQRTAMKRTPEEAIRFYSGFRQVG--RIHIVDLMGALK 58 Query: 58 GQPVNGEVVTAIAKRYPDLPIQIGGGIRTLETIEHYVRAGVSYVIIGTKAVKEPGFVTEA 117 V+ + K DLP+QIGGG+R +ETI Y R G+ Y I+GTKA+ + ++ EA Sbjct: 59 QDAQESTVIEKL-KSQTDLPLQIGGGLRNMETIRQYDRIGIDYFILGTKAILDTDWLKEA 117 Query: 118 CRAFPGKVIVGLDAKDGFVATDGWAEVSSVQAVDLARRFEADGVSAIVYTDIAKDGMMQG 177 R FPG++ VG DA++ + +GW E S + + R E ++ I+YTDI KDGM QG Sbjct: 118 VREFPGRIFVGTDARENDIYVNGWTENSDITIDEYIREIEGLDIAGIIYTDINKDGMNQG 177 Query: 178 CNVEATVALANASRIPVIASGGIHNIGDIQKLLDTNTPGIVGAITGRA 225 N E T + +R VIASGG+ N D+ KL G+ AI G+A Sbjct: 178 PNFENTRRINELTRHKVIASGGVRNKEDLDKL---GALGVRDAIVGKA 222 Lambda K H 0.320 0.138 0.405 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: 170 Number of extensions: 11 Number of successful extensions: 3 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: 247 Length of database: 233 Length adjustment: 23 Effective length of query: 224 Effective length of database: 210 Effective search space: 47040 Effective search space used: 47040 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: 46 (22.3 bits)
Align candidate WP_017550016.1 C792_RS0113615 (1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase)
to HMM TIGR00007 (hisA: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16))
# 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/TIGR00007.hmm # target sequence database: /tmp/gapView.527561.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00007 [M=231] Accession: TIGR00007 Description: TIGR00007: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-73 232.3 0.7 3.3e-73 232.1 0.7 1.0 1 NCBI__GCF_000330705.1:WP_017550016.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000330705.1:WP_017550016.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 232.1 0.7 3.3e-73 3.3e-73 1 227 [. 3 229 .. 3 232 .. 0.98 Alignments for each domain: == domain 1 score: 232.1 bits; conditional E-value: 3.3e-73 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfee.egaellHvVDLdgAkegekknlevikkiveele 72 iiPaiD+++G+ vrl qGd+d++t ++++p+ea++ ++ + ++H+VDL gA ++ +++++vi+k++++++ NCBI__GCF_000330705.1:WP_017550016.1 3 IIPAIDIIDGRNVRLKQGDYDQRTAMKRTPEEAIRFYSGfRQVGRIHIVDLMGALKQDAQESTVIEKLKSQTD 75 8************************************997789****************************** PP TIGR00007 73 vkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkeksel 145 +++q+GGG+R++e+++++ ++g+++ i+gt+a+ +++++ke+++e+ +i+v+ Da+e+++ v+GW+e+s++ NCBI__GCF_000330705.1:WP_017550016.1 76 LPLQIGGGLRNMETIRQYDRIGIDYFILGTKAILDTDWLKEAVREFP-GRIFVGTDARENDIYVNGWTENSDI 147 **********************************************9.************************* PP TIGR00007 146 slvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalkklgvkgvivG 218 ++ e ++++e l++++ii+Tdi+kdG+ +G+n+e t+++ + ++ +viasGGv+++ed+ +l +lgv+++ivG NCBI__GCF_000330705.1:WP_017550016.1 148 TIDEYIREIEGLDIAGIIYTDINKDGMNQGPNFENTRRINELTRHKVIASGGVRNKEDLDKLGALGVRDAIVG 220 ************************************************************************* PP TIGR00007 219 kAlyegklk 227 kA ++ +++ NCBI__GCF_000330705.1:WP_017550016.1 221 KASHNDSFW 229 ***999886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (233 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 20.41 // [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