Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_013419487.1 RVAN_RS09330 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_000166055.1:WP_013419487.1 Length = 253 Score = 162 bits (411), Expect = 5e-45 Identities = 102/256 (39%), Positives = 148/256 (57%), Gaps = 8/256 (3%) Query: 16 ASLIGGLRAQGVPAA-QIRASDPGAEQRAKIAGEFAIDVVESNAEAVADADVVVLSVKPQ 74 A L G LRA P A +R P A+ A + E I ++ + + DV+VL+VKPQ Sbjct: 4 ALLRGWLRAGFPPTAIAVREPQPSAQMTALLQ-EKGIPMLPED-----EPDVMVLAVKPQ 57 Query: 75 AMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPALLRQGASGLY 134 + V + + P +++SIAAG + + +VR MPN PA + +G +G + Sbjct: 58 ILPEVLPEVVNHVGPHTVVLSIAAGRTVSGIADQFRDGTAIVRAMPNLPAEVGRGVTGAF 117 Query: 135 ANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLMQAMTDAGEKL 194 NA V+ AQ E +LL AVG +W+DDE Q+DAVTAVSGSGPAY F L + + A E+ Sbjct: 118 PNANVTDAQRELCDKLLRAVGEVVWVDDEGQLDAVTAVSGSGPAYVFYLAECLAHAAEEA 177 Query: 195 GLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKSFQAN-GFEALV 253 GL + A +L T GA ++ S +E A+LR VTSP GTT AA+ + G +AL+ Sbjct: 178 GLPSDMAMKLARATVEGAGELMHRSPLEAAKLRENVTSPGGTTAAALAVLSKDEGLKALM 237 Query: 254 EQALNAASQRSAELAE 269 +A+ AA++RS EL++ Sbjct: 238 REAIAAAARRSRELSQ 253 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: 177 Number of extensions: 6 Number of successful extensions: 1 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: 253 Length adjustment: 25 Effective length of query: 248 Effective length of database: 228 Effective search space: 56544 Effective search space used: 56544 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_013419487.1 RVAN_RS09330 (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.1580.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-76 243.0 0.2 2.3e-76 242.9 0.2 1.0 1 lcl|NCBI__GCF_000166055.1:WP_013419487.1 RVAN_RS09330 pyrroline-5-carboxy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000166055.1:WP_013419487.1 RVAN_RS09330 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 242.9 0.2 2.3e-76 2.3e-76 9 263 .] 1 251 [. 1 251 [. 0.97 Alignments for each domain: == domain 1 score: 242.9 bits; conditional E-value: 2.3e-76 TIGR00112 9 mgeallsgllkkgakakkeilviers.eeklaalakelgvevtsdaeeavkeadvvllavKPqdleevl 76 mg all+g+l++g + ++ i v e++ +++++al++e g+ + + +e dv++lavKPq l+evl lcl|NCBI__GCF_000166055.1:WP_013419487.1 1 MGGALLRGWLRAGFP-PTAIAVREPQpSAQMTALLQEKGIPMLPE-----DEPDVMVLAVKPQILPEVL 63 9***********998.899******999999**********9999.....589**************** PP TIGR00112 77 aelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelve 145 e+ + + +++++Si+AG t++ + +++ + +++vR+mPN++a+vg+gvt+++ +++v+++q+el + lcl|NCBI__GCF_000166055.1:WP_013419487.1 64 PEVVN-HVGPHTVVLSIAAGRTVSGIADQFRDGTAIVRAMPNLPAEVGRGVTGAFPNANVTDAQRELCD 131 *9998.888************************************************************ PP TIGR00112 146 ellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklle 213 +ll+avG+vv+v+ e +ldavta+sGSgPA+vf+l+e+la+a+ ++GLp + a++la++t++Ga++l++ lcl|NCBI__GCF_000166055.1:WP_013419487.1 132 KLLRAVGEVVWVDdEGQLDAVTAVSGSGPAYVFYLAECLAHAAEEAGLPSDMAMKLARATVEGAGELMH 200 *************9******************************************************* PP TIGR00112 214 esgehpalLkdkVtsPgGtTiaglavLeekg.vrsavieaveaavkrseeL 263 +s ++a+L+++VtsPgGtT+a+lavL++++ +++ + ea+ aa++rs+eL lcl|NCBI__GCF_000166055.1:WP_013419487.1 201 RSPLEAAKLRENVTSPGGTTAAALAVLSKDEgLKALMREAIAAAARRSREL 251 ***************************98765999999***********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (253 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: 8.52 // [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