Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_012384256.1 BIND_RS06375 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_000019845.1:WP_012384256.1 Length = 276 Score = 161 bits (407), Expect = 2e-44 Identities = 101/261 (38%), Positives = 147/261 (56%), Gaps = 5/261 (1%) Query: 10 GAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADADVVVL 69 GAG M ++L+ G + G+PAA++ +P + + + + A+A DV+VL Sbjct: 18 GAGKMGSALLHGWLSLGLPAARVGVIEPHPSEPLRERAKTEGFTLTPPAKA---PDVLVL 74 Query: 70 SVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPALLRQG 129 ++KPQ ++ AL + LI+SI AG ++ + ++R MPN PA + G Sbjct: 75 AIKPQMLEEAAPALQAYVDENTLIISILAGKTIRNIAERFPRAGAIIRAMPNLPAAIGHG 134 Query: 130 ASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLMQAMTD 189 +GL A+A ++ Q A LL AVG WLDDE+ IDAVTA+SGSGPAY F L + ++ Sbjct: 135 MTGLAASAGLTPHQHALATTLLGAVGAVEWLDDESLIDAVTAISGSGPAYVFYLAECLSR 194 Query: 190 AGEKLGLSRETASRLTLQTAL-GAAQMALSSEVEPAELRRRVTSPNGTTEAAIKSFQA-N 247 AG LGL A RL T G A +A ++ PA+LR VTS GTT AA++ A N Sbjct: 195 AGAALGLPPAVAERLARATVEGGGALLAHEADTSPAQLRENVTSRGGTTAAALEILMAEN 254 Query: 248 GFEALVEQALNAASQRSAELA 268 G L+E+ AA +R+AEL+ Sbjct: 255 GLAPLIERTAAAAQKRAAELS 275 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: 197 Number of extensions: 8 Number of successful extensions: 4 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: 276 Length adjustment: 25 Effective length of query: 248 Effective length of database: 251 Effective search space: 62248 Effective search space used: 62248 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_012384256.1 BIND_RS06375 (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.298581.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-73 232.7 1.7 3.3e-73 232.6 1.7 1.0 1 NCBI__GCF_000019845.1:WP_012384256.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000019845.1:WP_012384256.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 232.6 1.7 3.3e-73 3.3e-73 3 263 .] 16 274 .. 14 274 .. 0.95 Alignments for each domain: == domain 1 score: 232.6 bits; conditional E-value: 3.3e-73 TIGR00112 3 iiGaGnmgeallsgllkkgakakkeilviers.eeklaalakelgvevtsdaeeavkeadvvllavKPqdlee 74 + GaG+mg+all+g+l+ g + ++++ vie++ +e l++ ak+ g + t +a k+ dv++la+KPq+lee NCBI__GCF_000019845.1:WP_012384256.1 16 LAGAGKMGSALLHGWLSLGLP-AARVGVIEPHpSEPLRERAKTEGFTLTPPA----KAPDVLVLAIKPQMLEE 83 67***************9887.899*****9999************999995....7899************* PP TIGR00112 75 vlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveel 147 ++ l+ +++l+iSilAG ti ++ + ++ +++R+mPN++a++g+g+t++aas+ +++q++l++ l NCBI__GCF_000019845.1:WP_012384256.1 84 AAPALQA-YVDENTLIISILAGKTIRNIAERFPRAGAIIRAMPNLPAAIGHGMTGLAASAGLTPHQHALATTL 155 ****999.66689************************************************************ PP TIGR00112 148 lkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesge.h 218 l avG v +++ e+l+davta+sGSgPA+vf+l+e+l +ag +lGLp + a++la++t++G ++ll+++ + + NCBI__GCF_000019845.1:WP_012384256.1 156 LGAVGAVEWLDdESLIDAVTAISGSGPAYVFYLAECLSRAGAALGLPPAVAERLARATVEGGGALLAHEADtS 228 ******************************************************************9987679 PP TIGR00112 219 palLkdkVtsPgGtTiaglavLe.ekgvrsavieaveaavkrseeL 263 pa+L+++Vts gGtT+a+l++L+ e+g+ ++++ aa kr+ eL NCBI__GCF_000019845.1:WP_012384256.1 229 PAQLRENVTSRGGTTAAALEILMaENGLAPLIERTAAAAQKRAAEL 274 ********************98725679**************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (276 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: 10.93 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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