Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate Dsui_0602 Dsui_0602 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__PS:Dsui_0602 Length = 270 Score = 229 bits (585), Expect = 4e-65 Identities = 128/268 (47%), Positives = 168/268 (62%), Gaps = 1/268 (0%) Query: 5 RIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADA 64 +I F+G GNMA +LIGGL +G A I + A+ R+K+ + + A D Sbjct: 2 KITFLGGGNMANALIGGLVNKGFAAGDIAVVELNADNRSKLEAAYGVRTFAGAEAAAWDC 61 Query: 65 DVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPA 124 DV+VL+VKPQ+MK + P LK +QL+VSIAAG+ ASL WLG R +VR MPNTPA Sbjct: 62 DVIVLAVKPQSMKEAIAPIGPHLK-DQLVVSIAAGLNLASLSRWLGGHRRLVRTMPNTPA 120 Query: 125 LLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLM 184 L+ G +GLYA +V AA A ++L AVG A+W DE+Q+DAVTAVSGSGPAY FL + Sbjct: 121 LIGAGVTGLYALPEVDAAGRAAAQRVLEAVGSAVWFADESQMDAVTAVSGSGPAYVFLFI 180 Query: 185 QAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKSF 244 +A+ AG+ LG E A RL ++T LGAAQ+A S + LR RVTS GTT AA+ Sbjct: 181 EALQQAGKDLGFDDEQARRLAIETVLGAAQLAAQSPDPASVLRERVTSKGGTTAAALAVM 240 Query: 245 QANGFEALVEQALNAASQRSAELAEQLG 272 + G +A + + AA R EL +QLG Sbjct: 241 ETAGVKAGIIAGVKAAEARGVELGQQLG 268 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: 199 Number of extensions: 10 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: 270 Length adjustment: 25 Effective length of query: 248 Effective length of database: 245 Effective search space: 60760 Effective search space used: 60760 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 Dsui_0602 Dsui_0602 (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.19484.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-83 263.8 4.7 1.1e-82 263.6 4.7 1.0 1 lcl|FitnessBrowser__PS:Dsui_0602 Dsui_0602 pyrroline-5-carboxylat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_0602 Dsui_0602 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 263.6 4.7 1.1e-82 1.1e-82 1 263 [] 3 263 .. 3 263 .. 0.98 Alignments for each domain: == domain 1 score: 263.6 bits; conditional E-value: 1.1e-82 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevla 77 i+++G+Gnm++al+ gl++kg + + +i v+e +++++ +l +++gv++ + ae+a+ + dv++lavKPq ++e++a lcl|FitnessBrowser__PS:Dsui_0602 3 ITFLGGGNMANALIGGLVNKGFA-AGDIAVVELNADNRSKLEAAYGVRTFAGAEAAAWDCDVIVLAVKPQSMKEAIA 78 78*****************9887.8**************************************************** PP TIGR00112 78 elkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellkavGkv 154 + + k++l++Si+AG++++ l+++l++++r+vR mPNt+a +gagvt+++a ev+++ ++ ++++l+avG++ lcl|FitnessBrowser__PS:Dsui_0602 79 PIGP--HLKDQLVVSIAAGLNLASLSRWLGGHRRLVRTMPNTPALIGAGVTGLYALPEVDAAGRAAAQRVLEAVGSA 153 9998..6689******************************************************************* PP TIGR00112 155 veve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalLkdkVtsPg 230 v+ + e+++davta+sGSgPA+vfl+ieal++ag lG++ e+a++la +t+ Gaa+l ++s + +++L+++Vts+g lcl|FitnessBrowser__PS:Dsui_0602 154 VWFAdESQMDAVTAVSGSGPAYVFLFIEALQQAGKDLGFDDEQARRLAIETVLGAAQLAAQSPDPASVLRERVTSKG 230 **999************************************************************************ PP TIGR00112 231 GtTiaglavLeekgvrsavieaveaavkrseeL 263 GtT+a+lav+e +gv++++i++v+aa +r eL lcl|FitnessBrowser__PS:Dsui_0602 231 GTTAAALAVMETAGVKAGIIAGVKAAEARGVEL 263 **************************9998776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (270 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: 7.90 // [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