Align Formiminoglutamic iminohydrolase (EC 3.5.3.13) (characterized)
to candidate AO356_09645 AO356_09645 N-formimino-L-glutamate deiminase
Query= reanno::pseudo5_N2C3_1:AO356_09645 (454 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_09645 Length = 454 Score = 923 bits (2385), Expect = 0.0 Identities = 454/454 (100%), Positives = 454/454 (100%) Query: 1 MSAFFAERALLPSGWAHDVRLEVDAKGVLTHIQAGSHADGAERLGGPLLPGMPNLHSHAF 60 MSAFFAERALLPSGWAHDVRLEVDAKGVLTHIQAGSHADGAERLGGPLLPGMPNLHSHAF Sbjct: 1 MSAFFAERALLPSGWAHDVRLEVDAKGVLTHIQAGSHADGAERLGGPLLPGMPNLHSHAF 60 Query: 61 QRAMAGLAEVAGNPNDSFWTWRDLMYRLVGKISPDQLGIIARQLYIEMLKAGYTSVAEFH 120 QRAMAGLAEVAGNPNDSFWTWRDLMYRLVGKISPDQLGIIARQLYIEMLKAGYTSVAEFH Sbjct: 61 QRAMAGLAEVAGNPNDSFWTWRDLMYRLVGKISPDQLGIIARQLYIEMLKAGYTSVAEFH 120 Query: 121 YVHHDTDGAPYADPAELALRISHAASAAGIGLTLLPVLYSHSGFGGQAPNDGQRRFINST 180 YVHHDTDGAPYADPAELALRISHAASAAGIGLTLLPVLYSHSGFGGQAPNDGQRRFINST Sbjct: 121 YVHHDTDGAPYADPAELALRISHAASAAGIGLTLLPVLYSHSGFGGQAPNDGQRRFINST 180 Query: 181 ENYLKLQSRLQPILAGQPAQALGLCFHSLRAVTPGQIQDVLAASDRDCPVHIHIAEQQKE 240 ENYLKLQSRLQPILAGQPAQALGLCFHSLRAVTPGQIQDVLAASDRDCPVHIHIAEQQKE Sbjct: 181 ENYLKLQSRLQPILAGQPAQALGLCFHSLRAVTPGQIQDVLAASDRDCPVHIHIAEQQKE 240 Query: 241 VDDCLSWSGARPLQWLYENTEVDQRWCLVHATHANAQEVSLMAKSRAIAGLCLTTEANLG 300 VDDCLSWSGARPLQWLYENTEVDQRWCLVHATHANAQEVSLMAKSRAIAGLCLTTEANLG Sbjct: 241 VDDCLSWSGARPLQWLYENTEVDQRWCLVHATHANAQEVSLMAKSRAIAGLCLTTEANLG 300 Query: 301 DGIFPAVDFLAQGGRLGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYRADQPMVGRT 360 DGIFPAVDFLAQGGRLGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYRADQPMVGRT Sbjct: 301 DGIFPAVDFLAQGGRLGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYRADQPMVGRT 360 Query: 361 LFDAALEGGAQALGQPVGALDIGKRADWLVLDGNDPYLATANGDGILNRWLFAGGDRQVR 420 LFDAALEGGAQALGQPVGALDIGKRADWLVLDGNDPYLATANGDGILNRWLFAGGDRQVR Sbjct: 361 LFDAALEGGAQALGQPVGALDIGKRADWLVLDGNDPYLATANGDGILNRWLFAGGDRQVR 420 Query: 421 DVMVGGRWVVRDGRHAGEEESARAFTQVLRELLD 454 DVMVGGRWVVRDGRHAGEEESARAFTQVLRELLD Sbjct: 421 DVMVGGRWVVRDGRHAGEEESARAFTQVLRELLD 454 Lambda K H 0.321 0.137 0.422 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: 961 Number of extensions: 32 Number of successful extensions: 1 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: 454 Length of database: 454 Length adjustment: 33 Effective length of query: 421 Effective length of database: 421 Effective search space: 177241 Effective search space used: 177241 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: 51 (24.3 bits)
Align candidate AO356_09645 AO356_09645 (N-formimino-L-glutamate deiminase)
to HMM TIGR02022 (hutF: formiminoglutamate deiminase (EC 3.5.3.13))
# 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.carbon/TIGR02022.hmm # target sequence database: /tmp/gapView.23587.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02022 [M=455] Accession: TIGR02022 Description: hutF: formiminoglutamate deiminase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-227 740.0 0.4 5.2e-227 739.9 0.4 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09645 AO356_09645 N-formimino-L-glutam Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09645 AO356_09645 N-formimino-L-glutamate deiminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 739.9 0.4 5.2e-227 5.2e-227 1 454 [. 1 453 [. 1 454 [] 0.99 Alignments for each domain: == domain 1 score: 739.9 bits; conditional E-value: 5.2e-227 TIGR02022 1 akvyfaerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanlHsHAFqr 63 ++++faerallp gwa++vrl+v+++G ++ +++g+ a++aerl+g++lpg++nlHsHAFqr lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09645 1 MSAFFAERALLPSGWAHDVRLEVDAKGVLTHIQAGSH-ADGAERLGGPLLPGMPNLHSHAFQR 62 5789****************************99998.************************* PP TIGR02022 64 alaGlaevagsgaDsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHa 126 a+aGlaevag+++DsFWtWR++mYrlv +++P+ql +iarqly+emlkaG+t+v+EFHY+HH+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09645 63 AMAGLAEVAGNPNDSFWTWRDLMYRLVGKISPDQLGIIARQLYIEMLKAGYTSVAEFHYVHHD 125 *************************************************************** PP TIGR02022 127 adGtpYadpaelaeriaaAAadaGigltlLpvlYahagFGgaaanegqrrfiddveaflrlve 189 +dG+pYadpaela ri++AA+ aGigltlLpvlY+h+gFGg+a+n+gqrrfi+++e++l+l++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09645 126 TDGAPYADPAELALRISHAASAAGIGLTLLPVLYSHSGFGGQAPNDGQRRFINSTENYLKLQS 188 *************************************************************** PP TIGR02022 190 alrkelaaqeearlGlaiHslRAvtaeelaavlqaserqlPvHiHvaEqqkEvddClaasgrr 252 +l++ la+q+++ lGl++HslRAvt+ ++++vl+as+r +PvHiH+aEqqkEvddCl +sg r lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09645 189 RLQPILAGQPAQALGLCFHSLRAVTPGQIQDVLAASDRDCPVHIHIAEQQKEVDDCLSWSGAR 251 *************************************************************** PP TIGR02022 253 PvewLldhaevdarwclvHatHltdeevkllaksgavaglCpttEanLgDGifpaadfvaagg 315 P++wL++++evd+rwclvHatH +++ev+l+aks+a+aglC+ttEanLgDGifpa+df+a+gg lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09645 252 PLQWLYENTEVDQRWCLVHATHANAQEVSLMAKSRAIAGLCLTTEANLGDGIFPAVDFLAQGG 314 *************************************************************** PP TIGR02022 316 rlgiGsDshvvvdvleElRllEygqRLrdraRnvlaageeasvaralydaAlaggaqalGlae 378 rlgiGsDshv+++v+eElR+lEygqRLrd++Rn+l++ ++++v+r+l+daAl ggaqalG+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09645 315 RLGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYRADQPMVGRTLFDAALEGGAQALGQPV 377 *************************************************************** PP TIGR02022 379 geleaGarADlltldledpslagakgdalldsllfaaekaavrdvvvaGrkvvrdgrHaleee 441 g+l G+rAD+l+ld++dp+la+a+gd +l+++lfa+++++vrdv+v+Gr+vvrdgrHa eee lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09645 378 GALDIGKRADWLVLDGNDPYLATANGDGILNRWLFAGGDRQVRDVMVGGRWVVRDGRHAGEEE 440 *************************************************************** PP TIGR02022 442 ierafakvlrall 454 ++raf++vlr+ll lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09645 441 SARAFTQVLRELL 453 **********996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (454 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: 00:00:00.01 # Mc/sec: 11.47 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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