Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_011883327.1 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_000016205.1:WP_011883327.1 Length = 270 Score = 221 bits (564), Expect = 1e-62 Identities = 129/269 (47%), Positives = 167/269 (62%), Gaps = 1/269 (0%) Query: 5 RIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADA 64 +IAFIG GNMAA+LIGGL +GV A + A D + RA+ A +F I + +AD Sbjct: 2 KIAFIGGGNMAAALIGGLVKRGVAADGLYAIDVNEDVRARAAQQFGIRTGAAVDATLADY 61 Query: 65 DVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPA 124 D +VL+VKPQ +K V QALAP LK QL++SIAAGI A L WLG VVR MPNTPA Sbjct: 62 DAIVLAVKPQVLKEVAQALAPHLK-SQLVISIAAGIRGADLARWLGGYTRVVRTMPNTPA 120 Query: 125 LLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLM 184 L+ G +GL A V A E A +L AVG +W DE Q+DAVTA+SGSGPAY F + Sbjct: 121 LVGMGVTGLAALPGVDATGRELASSVLGAVGEIVWFADEVQLDAVTAISGSGPAYVFYFI 180 Query: 185 QAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKSF 244 +A+ +A +LGL+ E L + T GAAQ+A S + LR RVTS GTT AA+ SF Sbjct: 181 EALQEAARRLGLNDEQGRALAVATFAGAAQLAAQSGEPASVLRERVTSKGGTTAAALASF 240 Query: 245 QANGFEALVEQALNAASQRSAELAEQLGQ 273 A + + + AA R+ E+ ++LG+ Sbjct: 241 DAQQVKEAIVRGALAAHARAQEMGDELGR 269 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: 186 Number of extensions: 8 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 WP_011883327.1 (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.4057.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-78 248.0 7.8 7.3e-78 247.8 7.8 1.0 1 lcl|NCBI__GCF_000016205.1:WP_011883327.1 pyrroline-5-carboxylate reductas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016205.1:WP_011883327.1 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 247.8 7.8 7.3e-78 7.3e-78 1 263 [] 3 263 .. 3 263 .. 0.98 Alignments for each domain: == domain 1 score: 247.8 bits; conditional E-value: 7.3e-78 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 ia+iG+Gnm++al+ gl+k+g++ ++ ++ i+ +e+ +a+ a+++g+++ +++++ ++ d ++lavKP lcl|NCBI__GCF_000016205.1:WP_011883327.1 3 IAFIGGGNMAAALIGGLVKRGVA-ADGLYAIDVNEDVRARAAQQFGIRTGAAVDATLADYDAIVLAVKP 70 89*****************9887.89******************************************* PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 q+l+ev++ l+ + k++l+iSi+AG++ ++l ++l++ +rvvR mPNt+a vg gvt++aa v++ lcl|NCBI__GCF_000016205.1:WP_011883327.1 71 QVLKEVAQALAP--HLKSQLVISIAAGIRGADLARWLGGYTRVVRTMPNTPALVGMGVTGLAALPGVDA 137 *********999..5689*************************************************** PP TIGR00112 139 eqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206 + +el++++l avG++v+ + e +ldavta+sGSgPA+vf++ieal++a+ +lGL+ e+ ++la +t++ lcl|NCBI__GCF_000016205.1:WP_011883327.1 138 TGRELASSVLGAVGEIVWFAdEVQLDAVTAISGSGPAYVFYFIEALQEAARRLGLNDEQGRALAVATFA 206 *******************99************************************************ PP TIGR00112 207 GaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 Gaa+l ++sge +++L+++Vts+gGtT+a+la++ +++v++a+ ++ aa +r++e+ lcl|NCBI__GCF_000016205.1:WP_011883327.1 207 GAAQLAAQSGEPASVLRERVTSKGGTTAAALASFDAQQVKEAIVRGALAAHARAQEM 263 ******************************************************986 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.87 // [ok]
This GapMind analysis is from Apr 10 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