Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate GFF2438 PGA1_c24700 pyrroline-5-carboxylate reductase ProC
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__Phaeo:GFF2438 Length = 275 Score = 181 bits (458), Expect = 2e-50 Identities = 111/267 (41%), Positives = 153/267 (57%), Gaps = 6/267 (2%) Query: 5 RIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADA 64 RIA +G G M ++++ G +GV + DP + G + + EA ADA Sbjct: 10 RIALLGCGKMGSAMLAGWLDRGVSPEAVWVIDPNPSDWLRQTG---VHINAPLPEAGADA 66 Query: 65 D-VVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTP 123 +V+++VKPQ M L E L +S+AAG A+ E+ LG P+VR MPNTP Sbjct: 67 PGIVLIAVKPQMMGEALPQLQQLGNGETLFISVAAGTSIATYESLLGAETPIVRAMPNTP 126 Query: 124 ALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLL 183 A + +G + + NA SA +A LL A+G + L EAQ+DAVT VSGSGPAY F L Sbjct: 127 AAVGRGITAIIGNASASADDVIRADALLKAIGQTVRLQSEAQMDAVTGVSGSGPAYVFHL 186 Query: 184 MQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKS 243 ++ + AGE GL E A +L T GA +A ++E PAELR VTSPNGTT+AA++ Sbjct: 187 IETLAAAGEAEGLPAELAMQLAKATVAGAGALAEAAEETPAELRVNVTSPNGTTQAALEV 246 Query: 244 F--QANGFEALVEQALNAASQRSAELA 268 + NGF L+ +A+ AAS RS EL+ Sbjct: 247 LMDEDNGFPPLLRRAVAAASNRSKELS 273 Lambda K H 0.315 0.127 0.348 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: 204 Number of extensions: 13 Number of successful extensions: 3 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: 273 Length of database: 275 Length adjustment: 25 Effective length of query: 248 Effective length of database: 250 Effective search space: 62000 Effective search space used: 62000 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 (21.6 bits) S2: 47 (22.7 bits)
Align candidate GFF2438 PGA1_c24700 (pyrroline-5-carboxylate reductase ProC)
to HMM TIGR00112 (proC: pyrroline-5-carboxylate reductase (EC 1.5.1.2))
# 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/TIGR00112.hmm # target sequence database: /tmp/gapView.8864.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00112 [M=263] Accession: TIGR00112 Description: proC: pyrroline-5-carboxylate reductase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-78 250.4 3.0 1.3e-78 250.2 3.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF2438 PGA1_c24700 pyrroline-5-carboxyl Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF2438 PGA1_c24700 pyrroline-5-carboxylate reductase ProC # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 250.2 3.0 1.3e-78 1.3e-78 1 263 [] 11 272 .. 11 272 .. 0.93 Alignments for each domain: == domain 1 score: 250.2 bits; conditional E-value: 1.3e-78 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkea.dvvllavKPqdleev 75 ia++G+G+mg+a+l+g+l +g++ ++ ++vi+++++ + ++gv+ +++ ea ++a +vl+avKPq++ e+ lcl|FitnessBrowser__Phaeo:GFF2438 11 IALLGCGKMGSAMLAGWLDRGVS-PEAVWVIDPNPSD---WLRQTGVHINAPLPEAGADApGIVLIAVKPQMMGEA 82 799****************9887.9*******88654...45566777777776666555279999********** PP TIGR00112 76 laelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellkav 151 l +l++ + e+l+iS++AG++i+++e+ll+ae+++vR+mPNt+a+vg+g+tai+ ++ +s+++ ++++llka+ lcl|FitnessBrowser__Phaeo:GFF2438 83 LPQLQQ-LGNGETLFISVAAGTSIATYESLLGAETPIVRAMPNTPAAVGRGITAIIGNASASADDVIRADALLKAI 157 *****9.66699**************************************************************** PP TIGR00112 152 Gkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalLkdkV 226 G++v+++ e+++davt++sGSgPA+vf+lie la+ag ++GLp+e+a++la++t++Ga++l e +e+pa+L+ +V lcl|FitnessBrowser__Phaeo:GFF2438 158 GQTVRLQsEAQMDAVTGVSGSGPAYVFHLIETLAAAGEAEGLPAELAMQLAKATVAGAGALAEAAEETPAELRVNV 233 **************************************************************************** PP TIGR00112 227 tsPgGtTiaglavL..eekgvrsavieaveaavkrseeL 263 tsP+GtT+a+l+vL e++g+ + +av aa++rs+eL lcl|FitnessBrowser__Phaeo:GFF2438 234 TSPNGTTQAALEVLmdEDNGFPPLLRRAVAAASNRSKEL 272 **************444567*****************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (275 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.80 // [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