Align 1-(5-phosphoribosyl)-5-[(5 phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate 201226 SO2069 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (NCBI ptt file)
Query= BRENDA::P10372 (245 letters) >FitnessBrowser__MR1:201226 Length = 245 Score = 301 bits (771), Expect = 8e-87 Identities = 149/244 (61%), Positives = 182/244 (74%) Query: 1 MIIPALDLIDGTVVRLHQGDYARQRDYGNDPLPRLQDYAAQGAGVLHLVDLTGAKDPAKR 60 MIIPA+DLIDG VVRL+QGDY +Q + PL +LQ Y AQ A LH+VDLTGAKDPAKR Sbjct: 1 MIIPAIDLIDGKVVRLYQGDYGQQTTFDLSPLAQLQSYQAQDASWLHIVDLTGAKDPAKR 60 Query: 61 QIPLIKTLVAGVNVPVQVGGGVRTEEDVAALLKAGVARVVIGSTAVKSPDVVKGWFERFG 120 Q LI L AG++ +QVGGG+RTEE VA LL GV RVVIGS AVK P++VKGWF +FG Sbjct: 61 QTALIAALTAGLSANIQVGGGIRTEEQVAELLSLGVKRVVIGSLAVKEPELVKGWFNKFG 120 Query: 121 AQALVLALDVRIDEHGTKQVAVSGWQENSGVSLEQLVETYLPVGLKHVLCTDISRDGTLA 180 +A+ LALD+ I G K VAVSGWQ G +LE +VE + VGLKH L TDISRDGTL Sbjct: 121 NEAICLALDINITPSGEKIVAVSGWQNGGGKNLESIVEDFSQVGLKHALVTDISRDGTLT 180 Query: 181 GSNVSLYEEVCARYPQIAFQSSGGIGDIDDIAALRGTGVRGVIVGRALLEGKFTVKEAIQ 240 G+N LY E+ +RYP IA+Q+SGGI ++D+AA+R +G G+I+G+ALL +F V EAIQ Sbjct: 181 GANTELYCELSSRYPNIAWQASGGIASLEDVAAVRDSGAAGIIIGKALLINQFNVAEAIQ 240 Query: 241 CWQN 244 CW N Sbjct: 241 CWPN 244 Lambda K H 0.319 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: 197 Number of extensions: 4 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: 245 Length of database: 245 Length adjustment: 24 Effective length of query: 221 Effective length of database: 221 Effective search space: 48841 Effective search space used: 48841 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 201226 SO2069 (phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (NCBI ptt file))
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.7485.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-76 243.3 0.4 1.4e-76 243.1 0.4 1.0 1 lcl|FitnessBrowser__MR1:201226 SO2069 phosphoribosylformimino-5 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:201226 SO2069 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (NCBI # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 243.1 0.4 1.4e-76 1.4e-76 1 230 [. 2 237 .. 2 238 .. 0.98 Alignments for each domain: == domain 1 score: 243.1 bits; conditional E-value: 1.4e-76 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveelevkvqvGG 79 iiPaiDl++Gkvvrl+qGd++++t+++ +pl++ ++++++ a++lH+VDL+gAk+ +k+++ +i+ ++ l++++qvGG lcl|FitnessBrowser__MR1:201226 2 IIPAIDLIDGKVVRLYQGDYGQQTTFDLSPLAQLQSYQAQDASWLHIVDLTGAKDPAKRQTALIAALTAGLSANIQVGG 80 8****************************************************************************** PP TIGR00007 80 GiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakeg.....evavkGWkekselslvelakk 153 GiR+ e+v++ll+lgv+rv+ig++av++pelvk +++++g+e i+++lD++ + vav+GW++ +l+++++ lcl|FitnessBrowser__MR1:201226 81 GIRTEEQVAELLSLGVKRVVIGSLAVKEPELVKGWFNKFGNEAICLALDINITpsgekIVAVSGWQNGGGKNLESIVED 159 **************************************************988778879******************** PP TIGR00007 154 leelgleeiilTdiekdGtlsGvnveltkelvke.aeveviasGGvssiedvkalkklgvkgvivGkAlyegklklke 230 ++++gl++ ++Tdi++dGtl+G n+el+ el+++ ++ +asGG++s edv a++++g++g+i+GkAl+ +++++ e lcl|FitnessBrowser__MR1:201226 160 FSQVGLKHALVTDISRDGTLTGANTELYCELSSRyPNIAWQASGGIASLEDVAAVRDSGAAGIIIGKALLINQFNVAE 237 **********************************9***************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (245 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: 8.69 // [ok]
This GapMind analysis is from Apr 09 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