Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate RR42_RS17360 RR42_RS17360 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__Cup4G11:RR42_RS17360 Length = 274 Score = 206 bits (524), Expect = 4e-58 Identities = 118/273 (43%), Positives = 162/273 (59%), Gaps = 1/273 (0%) Query: 1 MSTPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEA 60 + T F+G GNMA +LIGGL A+GVPA IR DP E +A++ + + + A Sbjct: 2 LKTLTFGFLGGGNMATALIGGLIARGVPATSIRVVDPFDEAQARLRRDLGVHAAGAPDTA 61 Query: 61 VADADVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMP 120 +DV+VL+VKPQ + AL P L + LIVS+AAGI A ++ W G +VR MP Sbjct: 62 FGKSDVLVLAVKPQQFREAAAALLPHLG-DSLIVSVAAGIRLADMQRWFGGRTRLVRAMP 120 Query: 121 NTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYF 180 NTPAL G +GL A A ++ + A L AVG W++ +AQIDAVTA+SGSGPAY Sbjct: 121 NTPALAGMGMTGLAAVAGLAQQDRDIASALAEAVGKCEWVEGDAQIDAVTAISGSGPAYV 180 Query: 181 FLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAA 240 F ++AM A +LGLS L ++T GAA +A SE + LR RVTS GTT AA Sbjct: 181 FYFIEAMEKAAVELGLSAAQGRALAVETFRGAAALAAQSEEPVSLLRERVTSKGGTTYAA 240 Query: 241 IKSFQANGFEALVEQALNAASQRSAELAEQLGQ 273 + + QA G +A+ AA++R+ E+ + G+ Sbjct: 241 LTAMQAAGIGEAFVKAMRAAAERATEMGAEFGK 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: 175 Number of extensions: 3 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 RR42_RS17360 RR42_RS17360 (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.2688.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-78 249.8 6.0 2e-78 249.7 6.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS17360 RR42_RS17360 pyrroline-5-carboxy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS17360 RR42_RS17360 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 249.7 6.0 2e-78 2e-78 2 263 .] 8 267 .. 7 267 .. 0.98 Alignments for each domain: == domain 1 score: 249.7 bits; conditional E-value: 2e-78 TIGR00112 2 aiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPq 70 +++G+Gnm++al+ gl+++g++ +++i v+++ +e+ a+l +lgv+++ + ++a ++dv++lavKPq lcl|FitnessBrowser__Cup4G11:RR42_RS17360 8 GFLGGGNMATALIGGLIARGVP-ATSIRVVDPFDEAQARLRRDLGVHAAGAPDTAFGKSDVLVLAVKPQ 75 79*****************998.8********************************************* PP TIGR00112 71 dleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevsee 139 +++e++a l + ++l++S++AG++++++++++++++r+vR+mPNt+a g g+t++aa + ++ lcl|FitnessBrowser__Cup4G11:RR42_RS17360 76 QFREAAAALLP--HLGDSLIVSVAAGIRLADMQRWFGGRTRLVRAMPNTPALAGMGMTGLAAVAGLAQQ 142 *******9988..6689**************************************************** PP TIGR00112 140 qkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkG 207 +++ +++l +avGk+ +ve ++++davta+sGSgPA+vf++iea+++a+v+lGL++++ ++la +t+ G lcl|FitnessBrowser__Cup4G11:RR42_RS17360 143 DRDIASALAEAVGKCEWVEgDAQIDAVTAISGSGPAYVFYFIEAMEKAAVELGLSAAQGRALAVETFRG 211 ********************************************************************* PP TIGR00112 208 aaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 aa+l ++s+e +lL+++Vts+gGtT a+l +++++g+ +a+ +a++aa++r++e+ lcl|FitnessBrowser__Cup4G11:RR42_RS17360 212 AAALAAQSEEPVSLLRERVTSKGGTTYAALTAMQAAGIGEAFVKAMRAAAERATEM 267 ********99******************************************9986 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: 10.80 // [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