Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate 6937805 Sama_1946 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq)
Query= ecocyc::PRIBFAICARPISOM-MONOMER (245 letters) >FitnessBrowser__SB2B:6937805 Length = 245 Score = 293 bits (749), Expect = 3e-84 Identities = 143/244 (58%), Positives = 183/244 (75%) Query: 1 MIIPALDLIDGTVVRLHQGDYGKQRDYGNDPLPRLQDYAAQGAEVLHLVDLTGAKDPAKR 60 MIIPA+DLIDG VVRL QGDY K+ ++ DP +L Y GA +LHLVDLTGAKDP KR Sbjct: 1 MIIPAIDLIDGQVVRLFQGDYAKKTEFSLDPKNQLLSYQQDGAALLHLVDLTGAKDPDKR 60 Query: 61 QIPLIKTLVAGVNVPVQVGGGVRSEEDVAALLEAGVARVVVGSTAVKSQDMVKGWFERFG 120 Q LI+ + A ++ P+QVGGG+RS DV ALL AGVARVV+GS AVKS ++V F+++G Sbjct: 61 QTKLIEEIAASLSTPLQVGGGIRSAADVDALLNAGVARVVIGSLAVKSPEVVLRLFDKYG 120 Query: 121 ADALVLALDVRIDEQGNKQVAVSGWQENSGVSLEQLVETYLPVGLKHVLCTDISRDGTLA 180 DA+ LALDV ID GNK VAV GWQ+ G SLE LV+T++P GLKH L TDISRDGT+ Sbjct: 121 GDAICLALDVNIDADGNKMVAVHGWQQGGGKSLESLVDTFMPAGLKHALVTDISRDGTMT 180 Query: 181 GSNVSLYEEVCARYPQVAFQSSGGIGDIDDVAALRGTGVRGVIVGRALLEGKFTVKEAIA 240 G+N +LY E+ R+ +V +Q+SGG+ +DDV A++ +G G+I+G+ALL G F+ KEAIA Sbjct: 181 GANTALYCELAERFNEVQWQASGGVATLDDVKAVKTSGASGIIIGKALLTGVFSAKEAIA 240 Query: 241 CWQN 244 CW N Sbjct: 241 CWPN 244 Lambda K H 0.318 0.137 0.397 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: 203 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: 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
Align candidate 6937805 Sama_1946 (1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq))
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.3221.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-75 239.2 0.3 2.5e-75 239.0 0.3 1.0 1 lcl|FitnessBrowser__SB2B:6937805 Sama_1946 1-(5-phosphoribosyl)-5 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937805 Sama_1946 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazo # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 239.0 0.3 2.5e-75 2.5e-75 1 230 [. 2 237 .. 2 238 .. 0.98 Alignments for each domain: == domain 1 score: 239.0 bits; conditional E-value: 2.5e-75 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveelevkvqv 77 iiPaiDl++G+vvrl+qGd++kkt +s dp ++ +++++ga llH+VDL+gAk+ k+++++i++i+ +l++++qv lcl|FitnessBrowser__SB2B:6937805 2 IIPAIDLIDGQVVRLFQGDYAKKTEFSLDPKNQLLSYQQDGAALLHLVDLTGAKDPDKRQTKLIEEIAASLSTPLQV 78 8**************************************************************************** PP TIGR00007 78 GGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakeg.....evavkGWkekselslve 149 GGGiRs+++v++ll++gv+rv+ig++av++pe+v +l++++g + i+++lD++ + vav+GW++ sl++ lcl|FitnessBrowser__SB2B:6937805 79 GGGIRSAADVDALLNAGVARVVIGSLAVKSPEVVLRLFDKYGGDAICLALDVNIDadgnkMVAVHGWQQGGGKSLES 155 ***************************************************9987778889**************** PP TIGR00007 150 lakkleelgleeiilTdiekdGtlsGvnveltkelvke.aeveviasGGvssiedvkalkklgvkgvivGkAlyegk 225 l+ ++ +gl++ ++Tdi++dGt++G n+ l+ el+++ +ev+ +asGGv++ +dvka+k++g++g+i+GkAl++g lcl|FitnessBrowser__SB2B:6937805 156 LVDTFMPAGLKHALVTDISRDGTMTGANTALYCELAERfNEVQWQASGGVATLDDVKAVKTSGASGIIIGKALLTGV 232 ***************************************************************************** PP TIGR00007 226 lklke 230 ++ ke lcl|FitnessBrowser__SB2B:6937805 233 FSAKE 237 99987 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 7.06 // [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