Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate Echvi_2635 Echvi_2635 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__Cola:Echvi_2635 Length = 271 Score = 141 bits (355), Expect = 2e-38 Identities = 84/267 (31%), Positives = 139/267 (52%), Gaps = 2/267 (0%) Query: 5 RIAFIGAGNMAASLIGGL-RAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVAD 63 ++ IG GNM + + ++ + + D E+ ++ V E + V Sbjct: 2 KVLVIGGGNMGLTYAEAIANSKFLKDKDLMILDNSKEKTEELRKRSHFAVFEKLEDCVPA 61 Query: 64 ADVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTP 123 ADV+ ++VKP A+ + + Q+ +S+ AG+ A+++ L + + VVR MPN P Sbjct: 62 ADVIFIAVKPYHANALMETMKDLTSEGQIFISLMAGVTIAAIQEGLNRKK-VVRAMPNLP 120 Query: 124 ALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLL 183 A + +G + A+ +VS + LL G ++ LD E IDA T +SGSGPAY F Sbjct: 121 AQVGKGLTSFTASDEVSRLELSTIENLLDTTGRSVRLDTENDIDASTGISGSGPAYIFYF 180 Query: 184 MQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKS 243 MQ+M +A K+G S+ + L QT GA ++ SS+++P RV S GTT AA+ S Sbjct: 181 MQSMLEAALKMGFSKHDSRVLVEQTFAGAVELFSSSDLDPEAWMNRVASKGGTTRAALDS 240 Query: 244 FQANGFEALVEQALNAASQRSAELAEQ 270 N + ++++A AA R+ EL ++ Sbjct: 241 MDDNNVKEMIKEAAYAAFNRAVELGKE 267 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: 126 Number of extensions: 7 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: 271 Length adjustment: 25 Effective length of query: 248 Effective length of database: 246 Effective search space: 61008 Effective search space used: 61008 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 Echvi_2635 Echvi_2635 (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.aa/TIGR00112.hmm # target sequence database: /tmp/gapView.14236.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-75 238.8 0.3 4.4e-75 238.7 0.3 1.0 1 lcl|FitnessBrowser__Cola:Echvi_2635 Echvi_2635 pyrroline-5-carboxyla Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2635 Echvi_2635 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 238.7 0.3 4.4e-75 4.4e-75 2 263 .] 4 264 .. 3 264 .. 0.98 Alignments for each domain: == domain 1 score: 238.7 bits; conditional E-value: 4.4e-75 TIGR00112 2 aiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleev 75 +iG+Gnmg ++++ +++ ++k++++ ++s+ek+++l k+ +v ++ e +v +adv+++avKP++++++ lcl|FitnessBrowser__Cola:Echvi_2635 4 LVIGGGNMGLTYAEAIANSKFLKDKDLMILDNSKEKTEELRKRSHFAVFEKLEDCVPAADVIFIAVKPYHANAL 77 69************************************************************************ PP TIGR00112 76 laelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellk 149 ++++k+ +++++++iS++AGvti+++++ l+ k+vvR+mPN++a+vg+g t+++as+evs + +++e+ll+ lcl|FitnessBrowser__Cola:Echvi_2635 78 METMKD-LTSEGQIFISLMAGVTIAAIQEGLNR-KKVVRAMPNLPAQVGKGLTSFTASDEVSRLELSTIENLLD 149 **9998.7779********************85.88*************************999********** PP TIGR00112 150 avGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalL 222 ++G v+++ e+++da+t++sGSgPA++f+++ ++ +a++k+G++++ ++ l+ qt++Ga++l + s+ +p+++ lcl|FitnessBrowser__Cola:Echvi_2635 150 TTGRSVRLDtENDIDASTGISGSGPAYIFYFMQSMLEAALKMGFSKHDSRVLVEQTFAGAVELFSSSDLDPEAW 223 ************************************************************************** PP TIGR00112 223 kdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 ++V s+gGtT a+l ++ +++v++++ ea aa +r+ eL lcl|FitnessBrowser__Cola:Echvi_2635 224 MNRVASKGGTTRAALDSMDDNNVKEMIKEAAYAAFNRAVEL 264 *************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (271 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: 10.77 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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