Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_012972065.1 ALVIN_RS14440 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_000025485.1:WP_012972065.1 Length = 276 Score = 258 bits (660), Expect = 8e-74 Identities = 139/274 (50%), Positives = 182/274 (66%), Gaps = 1/274 (0%) Query: 1 MSTPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEA 60 MST I FIG GNMA SLI GL A G I+ SDP E+R + + + +NAEA Sbjct: 1 MSTANIRFIGGGNMATSLIAGLIADGYAPQAIQVSDPSPERRHALQASLGVRALATNAEA 60 Query: 61 VADADVVVLSVKPQAMKAVCQALAPALKPEQ-LIVSIAAGIPCASLEAWLGQPRPVVRCM 119 +A A+ +VL VKPQ +VC LAP L ++ LIVS+ AG+P +L+ WLG P+VR M Sbjct: 61 LAGAETLVLCVKPQLAASVCAELAPLLDGQRPLIVSVMAGVPEQTLQRWLGASLPIVRAM 120 Query: 120 PNTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAY 179 PNTPA+++ GA GL+A+ +V A +A +L AVG+ W++DE+ IDAVTA+SGSGPAY Sbjct: 121 PNTPAMVQTGAIGLHASPEVDAEGRNRAETILRAVGLVRWVEDESHIDAVTAISGSGPAY 180 Query: 180 FFLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEA 239 FFL M+A+ A +LGL ETA LT+QTALGAA+MA+ S PA LR +VTSP GTTE Sbjct: 181 FFLFMEALEQAAIELGLDGETARLLTIQTALGAAKMAMESTDPPARLREQVTSPGGTTER 240 Query: 240 AIKSFQANGFEALVEQALNAASQRSAELAEQLGQ 273 A+ F ALVE+A AA R+ EL++ L + Sbjct: 241 ALAVFDEADLRALVERAARAARDRAVELSKTLSE 274 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: 192 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: 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_012972065.1 ALVIN_RS14440 (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.32392.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-81 258.8 0.8 3.7e-81 258.6 0.8 1.0 1 lcl|NCBI__GCF_000025485.1:WP_012972065.1 ALVIN_RS14440 pyrroline-5-carbox Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025485.1:WP_012972065.1 ALVIN_RS14440 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 258.6 0.8 3.7e-81 3.7e-81 1 263 [] 6 268 .. 6 268 .. 0.99 Alignments for each domain: == domain 1 score: 258.6 bits; conditional E-value: 3.7e-81 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 i +iG+Gnm+++l++gl++ g + ++ i v ++s+e+++al ++lgv++ ++++ea + a++++l vKP lcl|NCBI__GCF_000025485.1:WP_012972065.1 6 IRFIGGGNMATSLIAGLIADGYA-PQAIQVSDPSPERRHALQASLGVRALATNAEALAGAETLVLCVKP 73 78*****************9776.9******************************************** PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 q + +v+ael+ + + l++S++AGv+ ++l+++l+a+ ++vR+mPNt+a+v+ g++++ as ev++ lcl|NCBI__GCF_000025485.1:WP_012972065.1 74 QLAASVCAELAPLLDGQRPLIVSVMAGVPEQTLQRWLGASLPIVRAMPNTPAMVQTGAIGLHASPEVDA 142 ************9999***************************************************** PP TIGR00112 139 eqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206 e ++++e +l+avG v +ve e+++davta+sGSgPA++fl++eal++a+++lGL+ e+a+ l+ qt lcl|NCBI__GCF_000025485.1:WP_012972065.1 143 EGRNRAETILRAVGLVRWVEdESHIDAVTAISGSGPAYFFLFMEALEQAAIELGLDGETARLLTIQTAL 211 ********************************************************************* PP TIGR00112 207 GaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 Gaak+ +es++ pa+L+++VtsPgGtT ++lav+ e+++r+ v++a +aa +r+ eL lcl|NCBI__GCF_000025485.1:WP_012972065.1 212 GAAKMAMESTDPPARLREQVTSPGGTTERALAVFDEADLRALVERAARAARDRAVEL 268 *****************************************************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.22 // [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