Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate WP_011033450.1 MM_RS07770 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= reanno::BFirm:BPHYT_RS17685 (250 letters) >NCBI__GCF_000007065.1:WP_011033450.1 Length = 246 Score = 182 bits (463), Expect = 4e-51 Identities = 93/230 (40%), Positives = 146/230 (63%), Gaps = 5/230 (2%) Query: 3 LIPAIDLKDGQCVRLKQGDMDQATIFSEEPAAMARHWVDRGARRLHLVDLNGAFAGKPKN 62 +IPA+D++ G+CV+L QG + ++P A+A WV +GA+ LHLVDL+GA G+ KN Sbjct: 5 VIPAVDMRGGKCVQLVQGVPGSEIVSIDDPLAVALDWVSKGAKTLHLVDLDGAIEGERKN 64 Query: 63 EDAIRAIIEEVGGE-IPVQLGGGIRDLNTIERYLDDGLSYVIIGTAAVKNPGFLQDACTA 121 I I+ + + +Q+GGGIR L+ G+S +I+GTAA++NP ++ ++ Sbjct: 65 SPIIEKIVNTCKEKGVSIQVGGGIRSFEDAASLLEIGVSRIILGTAALQNPELVKQLSSS 124 Query: 122 FGG-HIIVGLDAKDGKVATDGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGIN 180 FG H+ V LDAK+GK++ GW++ ++ RKFE+ G S+++T+I +G++QG+N Sbjct: 125 FGSSHVNVALDAKNGKISIKGWTEECAQTPVEMGRKFEELGAGSLLFTNIDTEGLMQGVN 184 Query: 181 IEATVRLARAVKIPVIASGGLSNLTDIESLCEVEDEGIEGVICGRAIYSG 230 T L +V IPVIASGG+S L DI++L + G GV+ G A+Y G Sbjct: 185 PVPTKELVESVSIPVIASGGVSTLEDIKTL---KKTGAAGVVVGSALYMG 231 Score = 33.9 bits (76), Expect = 3e-06 Identities = 31/121 (25%), Positives = 55/121 (45%), Gaps = 7/121 (5%) Query: 6 AIDLKDGQCVRLKQGDMDQATIFSEEPAAMARHWVDRGARRLHLVDLNGAFAGKPKNEDA 65 A+D K+G+ + +K + A + P M R + + GA L +++ + N Sbjct: 133 ALDAKNGK-ISIKGWTEECA----QTPVEMGRKFEELGAGSLLFTNIDTEGLMQGVNPVP 187 Query: 66 IRAIIEEVGGEIPVQLGGGIRDLNTIERYLDDGLSYVIIGTAAVKNPGFLQDACTAFGGH 125 + ++E V IPV GG+ L I+ G + V++G+A L++A A G Sbjct: 188 TKELVESVS--IPVIASGGVSTLEDIKTLKKTGAAGVVVGSALYMGRFTLEEAINAALGD 245 Query: 126 I 126 I Sbjct: 246 I 246 Lambda K H 0.319 0.140 0.410 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: 180 Number of extensions: 8 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 250 Length of database: 246 Length adjustment: 24 Effective length of query: 226 Effective length of database: 222 Effective search space: 50172 Effective search space used: 50172 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 (21.7 bits) S2: 46 (22.3 bits)
Align candidate WP_011033450.1 MM_RS07770 (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.22606.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-85 271.1 0.6 4.7e-85 270.9 0.6 1.0 1 lcl|NCBI__GCF_000007065.1:WP_011033450.1 MM_RS07770 1-(5-phosphoribosyl)- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007065.1:WP_011033450.1 MM_RS07770 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 270.9 0.6 4.7e-85 4.7e-85 1 231 [] 5 238 .. 5 238 .. 0.98 Alignments for each domain: == domain 1 score: 270.9 bits; conditional E-value: 4.7e-85 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 +iPa+D++ Gk+v+lvqG ++++ v ddpl++a ++ ++ga++lH+VDLdgA+ege+kn+++i+kiv+ lcl|NCBI__GCF_000007065.1:WP_011033450.1 5 VIPAVDMRGGKCVQLVQGVPGSEIVSIDDPLAVALDWVSKGAKTLHLVDLDGAIEGERKNSPIIEKIVN 73 89*****************************************************************98 PP TIGR00007 70 ele...vkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegeva 135 +++ v++qvGGGiRs+e++++lle+gv+r+i+gtaa++npelvk+l +++gs+++ v+lDak+g+++ lcl|NCBI__GCF_000007065.1:WP_011033450.1 74 TCKekgVSIQVGGGIRSFEDAASLLEIGVSRIILGTAALQNPELVKQLSSSFGSSHVNVALDAKNGKIS 142 77622278************************************************************* PP TIGR00007 136 vkGWkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedv 204 +kGW+e+ ++ve+ +k+eelg+ ++++T+i+++G ++Gvn tkelv++++++viasGGvs+ ed+ lcl|NCBI__GCF_000007065.1:WP_011033450.1 143 IKGWTEECAQTPVEMGRKFEELGAGSLLFTNIDTEGLMQGVNPVPTKELVESVSIPVIASGGVSTLEDI 211 ********************************************************************* PP TIGR00007 205 kalkklgvkgvivGkAlyegklklkea 231 k+lkk+g++gv+vG+Aly g+++l+ea lcl|NCBI__GCF_000007065.1:WP_011033450.1 212 KTLKKTGAAGVVVGSALYMGRFTLEEA 238 ***********************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (246 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: 9.32 // [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