Align Formiminoglutamase (EC 3.5.3.8) (characterized)
to candidate RR42_RS14625 RR42_RS14625 formimidoylglutamase
Query= reanno::Koxy:BWI76_RS08725 (318 letters) >FitnessBrowser__Cup4G11:RR42_RS14625 Length = 312 Score = 244 bits (624), Expect = 1e-69 Identities = 150/310 (48%), Positives = 184/310 (59%), Gaps = 8/310 (2%) Query: 8 PAALWQGRDDSAEAANALRLFQTIVRAERFEPEMLAGDIALLGFACDEGVRRNKGRTGAE 67 P ++W+GR D+ E + RLF +VRA+ E + G LLGF CD GV RN GR GA Sbjct: 5 PGSIWRGRSDAGELGDTRRLFH-VVRAQG--AERVPGAPVLLGFCCDAGVLRNLGRPGAA 61 Query: 68 RGPETLRRALANMASHDGHDRCVDMGTIHVADDALEAAQQALREAVTACQRAGKRTLVLG 127 GP +RRALA + +H G D G + D LE AQQAL AV A G LVLG Sbjct: 62 GGPREIRRALAGIPAH-GLAAFHDAGDVVCHDGDLETAQQALATAVAAELAQGAFPLVLG 120 Query: 128 GGHETAFGHGAGV---LDAFPGE-EVGIINLDAHLDLRIADRASSGTPFRQLALACEAQR 183 GGHE A+G G+ LDA V +INLDAH DLR SSGTPF Q+A AC + Sbjct: 121 GGHEIAWGTWQGLRAHLDARGDHGRVLVINLDAHFDLRTGRPGSSGTPFDQIAQACHERG 180 Query: 184 RAFHYACIGVSRAANTQALLDEAARRGVTIIEDLDVLNAFEARAIPELARNIARYDRLYL 243 + F YAC+GVSR NT AL A GV +ED+ + + EL + D +YL Sbjct: 181 QRFEYACLGVSRLGNTAALFAHAQALGVHYVEDVQMQERHLDARLAELQGLMDAVDHVYL 240 Query: 244 TIDLDVLPAREMPAVSAPAALGIPLATLLRIVEPLCRSGKLQAVDLVEFNPQYDIDSQGA 303 TIDLDVLPA MPAVSAPA G+PL + +V + SGKL+ DL EFNP YD D+ GA Sbjct: 241 TIDLDVLPAAVMPAVSAPAPYGVPLPVVEEVVALVRASGKLRVADLAEFNPLYDRDACGA 300 Query: 304 RAAARLAWQI 313 RAAARLA+++ Sbjct: 301 RAAARLAYRL 310 Lambda K H 0.322 0.135 0.408 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: 327 Number of extensions: 15 Number of successful extensions: 4 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: 318 Length of database: 312 Length adjustment: 27 Effective length of query: 291 Effective length of database: 285 Effective search space: 82935 Effective search space used: 82935 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate RR42_RS14625 RR42_RS14625 (formimidoylglutamase)
to HMM TIGR01227 (hutG: formimidoylglutamase (EC 3.5.3.8))
# 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/TIGR01227.hmm # target sequence database: /tmp/gapView.30147.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01227 [M=307] Accession: TIGR01227 Description: hutG: formimidoylglutamase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.9e-91 290.1 0.1 1.1e-90 289.9 0.1 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS14625 RR42_RS14625 formimidoylglutamas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS14625 RR42_RS14625 formimidoylglutamase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 289.9 0.1 1.1e-90 1.1e-90 1 304 [. 9 309 .. 9 312 .] 0.95 Alignments for each domain: == domain 1 score: 289.9 bits; conditional E-value: 1.1e-90 TIGR01227 1 lqgrldleeaskkrrdeqvakvvdlveledaqdekgvaliGvaldkgvirnkGrtGAkeaPsairqala 69 + gr d e ++ rr ++v++ + + + +++l+G+ +d+gv rn Gr GA +P ir+ala lcl|FitnessBrowser__Cup4G11:RR42_RS14625 9 WRGRSDAGELGDTRRLFHVVRAQGA-----ERVPGAPVLLGFCCDAGVLRNLGRPGAAGGPREIRRALA 72 7889999999999999999988877.....455889********************************* PP TIGR01227 70 nlgdlvasealyDlGdivlegddlvdaqkevaqavaelladarvvvllGGdneiayatikalaqa..ak 136 + ++ a D+Gd+v++++dl+ aq+++a ava+ la+++ +++lGG++eia+ t ++l+++ a+ lcl|FitnessBrowser__Cup4G11:RR42_RS14625 73 GI-PAHGLAAFHDAGDVVCHDGDLETAQQALATAVAAELAQGAFPLVLGGGHEIAWGTWQGLRAHldAR 140 **.6678899*******************************************************8877 PP TIGR01227 137 gek.riGvinfDAHfDlRavederptsGTpfrqlldeeqaed..fhlivlGirrfsntqalfdyakkkg 202 g++ r+ vin+DAHfDlR+ +sGTpf q+++++ + + f++++lG++r++nt+alf++a+ +g lcl|FitnessBrowser__Cup4G11:RR42_RS14625 141 GDHgRVLVINLDAHFDLRTGR--PGSSGTPFDQIAQACHERGqrFEYACLGVSRLGNTAALFAHAQALG 207 66689*************988..889****************999************************ PP TIGR01227 203 vryvtddalaelsletikdileefldevDfiyltvdlDVldaasAPGvsApaagGleleellelvkria 271 v+yv+d +++e +l+ ++ l+ ++d vD++ylt+dlDVl+aa P vsApa+ G+ l++++e+v + lcl|FitnessBrowser__Cup4G11:RR42_RS14625 208 VHYVEDVQMQERHLDARLAELQGLMDAVDHVYLTIDLDVLPAAVMPAVSAPAPYGVPLPVVEEVVALVR 276 ********************************************************************* PP TIGR01227 272 asdkvrgveivEvnPtlDaddrTarlaArlvah 304 as+k+r+++++E+nP +D d ar+aArl lcl|FitnessBrowser__Cup4G11:RR42_RS14625 277 ASGKLRVADLAEFNPLYDRDACGARAAARLAYR 309 *****************************9765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (307 nodes) Target sequences: 1 (312 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: 7.99 // [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