Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate GFF282 Psest_0283 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__psRCH2:GFF282 Length = 274 Score = 389 bits (998), Expect = e-113 Identities = 207/274 (75%), Positives = 235/274 (85%), Gaps = 1/274 (0%) Query: 1 MSTPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEA 60 M +PRIAFIGAGNMAASLIGGLRAQGV A IRASDPGAEQRAKI+ E I NA+A Sbjct: 1 MISPRIAFIGAGNMAASLIGGLRAQGVAAEAIRASDPGAEQRAKISAEHGIQTFAQNADA 60 Query: 61 VADADVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLG-QPRPVVRCM 119 +A ADVVVLSVKPQ M++VC+ L P L LIVSIAAGI C SL+ WLG +P+ +VRCM Sbjct: 61 LAGADVVVLSVKPQVMQSVCRDLVPHLDHAPLIVSIAAGISCDSLQRWLGPRPQAIVRCM 120 Query: 120 PNTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAY 179 PNTPALLRQG SGL+ANAQVSA Q +QA QLLSAVGIALWL++E IDAVTAVSGSGPAY Sbjct: 121 PNTPALLRQGVSGLFANAQVSAEQKQQAEQLLSAVGIALWLEEERLIDAVTAVSGSGPAY 180 Query: 180 FFLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEA 239 FFLL++AMT AGE+LGL R+TA++LT+QTALGAA+MA S+V+ AELRRRVTSPNGTTEA Sbjct: 181 FFLLIEAMTAAGEQLGLPRDTAAQLTMQTALGAARMACESDVDAAELRRRVTSPNGTTEA 240 Query: 240 AIKSFQANGFEALVEQALNAASQRSAELAEQLGQ 273 AIK+FQA GFE LV+QALNAA+QRSAELAEQLGQ Sbjct: 241 AIKAFQAGGFERLVQQALNAAAQRSAELAEQLGQ 274 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: 291 Number of extensions: 6 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: 273 Length of database: 274 Length adjustment: 25 Effective length of query: 248 Effective length of database: 249 Effective search space: 61752 Effective search space used: 61752 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 GFF282 Psest_0283 (pyrroline-5-carboxylate reductase)
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.16689.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-83 264.2 5.2 8.2e-83 264.0 5.2 1.0 1 lcl|FitnessBrowser__psRCH2:GFF282 Psest_0283 pyrroline-5-carboxyla Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF282 Psest_0283 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 264.0 5.2 8.2e-83 8.2e-83 1 263 [] 6 268 .. 6 268 .. 0.98 Alignments for each domain: == domain 1 score: 264.0 bits; conditional E-value: 8.2e-83 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevl 76 ia+iGaGnm+++l+ gl ++g++ ++ i ++ +e++a+ +e g+++ ++++ a + advv+l+vKPq++++v+ lcl|FitnessBrowser__psRCH2:GFF282 6 IAFIGAGNMAASLIGGLRAQGVA-AEAIRASDPGAEQRAKISAEHGIQTFAQNADALAGADVVVLSVKPQVMQSVC 80 89***************999887.899************************************************* PP TIGR00112 77 aelkseektkeklliSilAGvtiekleqlleae.krvvRvmPNtaakvgagvtaiaassevseeqkelveellkav 151 ++l + ++ l++Si+AG++++ l+++l+ + +++vR+mPNt+a +++gv++++a+++vs+eqk+++e+ll+av lcl|FitnessBrowser__psRCH2:GFF282 81 RDLVP-HLDHAPLIVSIAAGISCDSLQRWLGPRpQAIVRCMPNTPALLRQGVSGLFANAQVSAEQKQQAEQLLSAV 155 ****9.66699*******************988899**************************************** PP TIGR00112 152 Gkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalLkdkV 226 G ++++e e+l+davta+sGSgPA++flliea+ +ag +lGLpr++a +l++qt Gaa++ es+ ++a+L+ +V lcl|FitnessBrowser__psRCH2:GFF282 156 GIALWLEeERLIDAVTAVSGSGPAYFFLLIEAMTAAGEQLGLPRDTAAQLTMQTALGAARMACESDVDAAELRRRV 231 *******9999***************************************************************** PP TIGR00112 227 tsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 tsP+GtT a++++++++g+++ v++a++aa++rs eL lcl|FitnessBrowser__psRCH2:GFF282 232 TSPNGTTEAAIKAFQAGGFERLVQQALNAAAQRSAEL 268 **********************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (274 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: 11.21 // [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