Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate Ac3H11_788 Pyrroline-5-carboxylate reductase (EC 1.5.1.2)
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_788 Length = 281 Score = 211 bits (537), Expect = 1e-59 Identities = 120/269 (44%), Positives = 165/269 (61%), Gaps = 2/269 (0%) Query: 4 PRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVAD 63 P IAFIG GNMA+++IGGL QG PA+QI +P A R + F + A+ Sbjct: 14 PTIAFIGGGNMASAIIGGLIGQGHPASQIEVVEPYAPTREALLKNFGLTAQPEAGPALQR 73 Query: 64 ADVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTP 123 A +VV +VKPQ K A A A P+ L +S+AAGI S+ WLG R VVR MPNTP Sbjct: 74 ASIVVWAVKPQTFKDAA-AQARAHTPQALHLSVAAGIRSDSIAQWLGTER-VVRTMPNTP 131 Query: 124 ALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLL 183 AL+ +G S +YA V+ A+ + ++++ G LW++ E Q+DAVTA+SGSGPAY F Sbjct: 132 ALVGKGMSAIYARPAVTPAERQSVEAIMASTGEFLWVESETQLDAVTALSGSGPAYVFYF 191 Query: 184 MQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKS 243 ++AM AG +GLS A +L + T +GA+++A S PA LR RVTS GTT AA++S Sbjct: 192 LEAMARAGVGMGLSDAQAHQLAVGTFVGASELARRSHEPPAVLRERVTSKGGTTYAALQS 251 Query: 244 FQANGFEALVEQALNAASQRSAELAEQLG 272 +A+G E A+ AA +R+ EL + G Sbjct: 252 MEASGVSQAFEAAMRAAEKRANELGNEFG 280 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: 219 Number of extensions: 9 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: 281 Length adjustment: 25 Effective length of query: 248 Effective length of database: 256 Effective search space: 63488 Effective search space used: 63488 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 Ac3H11_788 (Pyrroline-5-carboxylate reductase (EC 1.5.1.2))
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.10470.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-83 263.9 4.4 1e-82 263.7 4.4 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_788 Pyrroline-5-carboxylate reductas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_788 Pyrroline-5-carboxylate reductase (EC 1.5.1.2) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 263.7 4.4 1e-82 1e-82 1 263 [] 16 275 .. 16 275 .. 0.98 Alignments for each domain: == domain 1 score: 263.7 bits; conditional E-value: 1e-82 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvv 63 ia+iG+Gnm++a++ gl+ +g + +++i v+e+ ++ ++al+k++g +++ +a a + a++v lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_788 16 IAFIGGGNMASAIIGGLIGQGHP-ASQIEVVEPYAPTREALLKNFGLTAQPEAGPALQRASIV 77 89******************988.8************************************** PP TIGR00112 64 llavKPqdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgag 126 + avKPq +++++a+ + +t ++l +S++AG++ + + q+l+ ++rvvR mPNt+a vg+g lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_788 78 VWAVKPQTFKDAAAQARA--HTPQALHLSVAAGIRSDSIAQWLG-TERVVRTMPNTPALVGKG 137 *************97665..6799*******************7.589*************** PP TIGR00112 127 vtaiaassevseeqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagv 188 ++ai+a+ +v++++++ ve++++++G+ ++ve e +ldavtalsGSgPA+vf+++ea+a+agv lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_788 138 MSAIYARPAVTPAERQSVEAIMASTGEFLWVEsETQLDAVTALSGSGPAYVFYFLEAMARAGV 200 *************************************************************** PP TIGR00112 189 klGLpreeakelaaqtlkGaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavie 251 +GL+ ++a +la t+ Ga++l +s+e pa+L+++Vts+gGtT a+l+++e++gv +a+++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_788 201 GMGLSDAQAHQLAVGTFVGASELARRSHEPPAVLRERVTSKGGTTYAALQSMEASGVSQAFEA 263 *************************************************************** PP TIGR00112 252 aveaavkrseeL 263 a++aa kr++eL lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_788 264 AMRAAEKRANEL 275 *********998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (281 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.78 // [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