Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_013841339.1 DESRU_RS06610 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= reanno::azobra:AZOBR_RS01680 (249 letters) >NCBI__GCF_000215085.1:WP_013841339.1 Length = 243 Score = 242 bits (618), Expect = 4e-69 Identities = 126/238 (52%), Positives = 166/238 (69%) Query: 1 MIIYPAIDLKDGACVRLLRGEMSQATVFNTEPADQARLFESQGFEWLHLVDLNGAFEGKP 60 MII+PAIDLK+G CVRLL G M ATV++ +P AR ++ QG ++H+VDL+GAF GKP Sbjct: 1 MIIFPAIDLKEGQCVRLLEGRMDSATVYSRDPGGTARNWQEQGASFIHVVDLDGAFAGKP 60 Query: 61 VNGKAVESILGAVAIPVQLGGGIRDLKTIAHWLEKGVSRVILGTVALREPELVREACREF 120 N +A+ IL AV +PVQ+GGGIRDL+T+ GV+RVILG+ A+ +PELV EA R + Sbjct: 61 RNREAIRQILEAVEVPVQVGGGIRDLETMEELFSMGVNRVILGSAAILKPELVAEAGRRY 120 Query: 121 PGKVAVGIDAREGYVAVAGWAETSTIKALDLALKFEDSGVAAIIYTDINRDGAMGGVNVE 180 KV VGIDAR+G VA+ GW ET + AL LA + ++ GV I++TDI RDG + G N+ Sbjct: 121 GAKVLVGIDARDGRVAIQGWGETVSKTALQLAREVKELGVQRIVFTDIRRDGRLSGPNLG 180 Query: 181 ATSDLAFHLTTPVIASGGVSSIDDLIALKKEEDTGIEGVICGRALYDGRIDPKTALDL 238 AT +LA VIASGGVSS++D+ A+K E G+EG I G+ALY G + AL L Sbjct: 181 ATGELARDSGLKVIASGGVSSLEDIRAVKALEKDGVEGAIVGKALYTGAVKLPEALAL 238 Lambda K H 0.318 0.138 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: 230 Number of extensions: 7 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: 249 Length of database: 243 Length adjustment: 24 Effective length of query: 225 Effective length of database: 219 Effective search space: 49275 Effective search space used: 49275 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
Align candidate WP_013841339.1 DESRU_RS06610 (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.97254.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-86 275.4 0.5 2.3e-86 275.2 0.5 1.0 1 NCBI__GCF_000215085.1:WP_013841339.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000215085.1:WP_013841339.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 275.2 0.5 2.3e-86 2.3e-86 1 230 [. 3 234 .. 3 235 .. 0.97 Alignments for each domain: == domain 1 score: 275.2 bits; conditional E-value: 2.3e-86 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveelev 73 i+PaiDlkeG++vrl++G++d+ tvys+dp +a++++e+ga+++HvVDLdgA++g+++n+e+i++i+e++ev NCBI__GCF_000215085.1:WP_013841339.1 3 IFPAIDLKEGQCVRLLEGRMDSATVYSRDPGGTARNWQEQGASFIHVVDLDGAFAGKPRNREAIRQILEAVEV 75 89*********************************************************************** PP TIGR00007 74 kvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkeksels 146 +vqvGGGiR+le++e+l+++gv+rvi+g+aa+ +pelv+e+ +++g k++v++Da++g+va++GW e+ + + NCBI__GCF_000215085.1:WP_013841339.1 76 PVQVGGGIRDLETMEELFSMGVNRVILGSAAILKPELVAEAGRRYG-AKVLVGIDARDGRVAIQGWGETVSKT 147 **********************************************.99************************ PP TIGR00007 147 lvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalkk...lgvkgvi 216 +++la++++elg+++i++Tdi +dG lsG+n+ +t el++ + +viasGGvss ed++a+k+ gv+g+i NCBI__GCF_000215085.1:WP_013841339.1 148 ALQLAREVKELGVQRIVFTDIRRDGRLSGPNLGATGELARDSGLKVIASGGVSSLEDIRAVKAlekDGVEGAI 220 *********************************************************98777655599***** PP TIGR00007 217 vGkAlyegklklke 230 vGkAly+g +kl e NCBI__GCF_000215085.1:WP_013841339.1 221 VGKALYTGAVKLPE 234 ********999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (243 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: 12.33 // [ok]
This GapMind analysis is from Jul 25 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