Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_018232723.1 THITHI_RS0108825 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_000378965.1:WP_018232723.1 Length = 275 Score = 263 bits (671), Expect = 4e-75 Identities = 150/270 (55%), Positives = 189/270 (70%), Gaps = 2/270 (0%) Query: 6 IAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAE-AVADA 64 IAFIGAGNMA SLIGGL G P + A DP A QR ++ + V ++A+ AVA A Sbjct: 5 IAFIGAGNMARSLIGGLIQDGWPEDALWAVDPDAAQREGVSRRWPRVHVHADADQAVAHA 64 Query: 65 DVVVLSVKPQAMKAVCQALAPALKPE-QLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTP 123 DV+VL+VKPQ + V + LA A++ L+VSIAAG+ +E WLG PVVRCMPNTP Sbjct: 65 DVLVLAVKPQVLGGVARGLAGAVQARGPLVVSIAAGVRGEDIERWLGGDLPVVRCMPNTP 124 Query: 124 ALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLL 183 AL+ GA+ L ANA+VS+ Q A +L AVG+ +WLDDEA +DAVTA+SGSGPAY FL+ Sbjct: 125 ALVGSGATALVANARVSSDQKAVAESILRAVGLTVWLDDEAALDAVTALSGSGPAYCFLV 184 Query: 184 MQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKS 243 M+AM DAG +LGL RETA L LQTA GAA++AL SE + A LR RVTS GTTE A++ Sbjct: 185 MEAMEDAGVQLGLPRETARLLALQTAFGAAKLALESEEDAATLRARVTSRGGTTEQALQV 244 Query: 244 FQANGFEALVEQALNAASQRSAELAEQLGQ 273 ++ G L+ +AL AA RS ELA+QLG+ Sbjct: 245 LESGGLRELLARALTAARDRSRELADQLGR 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: 195 Number of extensions: 4 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: 275 Length adjustment: 25 Effective length of query: 248 Effective length of database: 250 Effective search space: 62000 Effective search space used: 62000 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_018232723.1 THITHI_RS0108825 (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.2114067.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-84 268.7 0.1 3.5e-84 268.5 0.1 1.0 1 NCBI__GCF_000378965.1:WP_018232723.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000378965.1:WP_018232723.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 268.5 0.1 3.5e-84 3.5e-84 1 263 [] 5 268 .. 5 268 .. 0.96 Alignments for each domain: == domain 1 score: 268.5 bits; conditional E-value: 3.5e-84 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelg.vevtsdaeeavkeadvvllavKPqdl 72 ia+iGaGnm+++l+ gl++ g + ++ ++ +++ +++++ + v+v++da++av++adv++lavKPq+l NCBI__GCF_000378965.1:WP_018232723.1 5 IAFIGAGNMARSLIGGLIQDGWP-EDALWAVDPDAAQREGVSRRWPrVHVHADADQAVAHADVLVLAVKPQVL 76 89******************988.6888888888666666666554499************************ PP TIGR00112 73 eevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelve 145 v++ l++ ++++ l++Si+AGv+ e++e++l+++ +vvR+mPNt+a vg+g+ta++a+++vs++qk+ +e NCBI__GCF_000378965.1:WP_018232723.1 77 GGVARGLAGAVQARGPLVVSIAAGVRGEDIERWLGGDLPVVRCMPNTPALVGSGATALVANARVSSDQKAVAE 149 *********9999************************************************************ PP TIGR00112 146 ellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesge 217 ++l+avG +v+++ e+ ldavtalsGSgPA+ fl++ea++dagv+lGLpre+a+ la qt Gaakl es+e NCBI__GCF_000378965.1:WP_018232723.1 150 SILRAVGLTVWLDdEAALDAVTALSGSGPAYCFLVMEAMEDAGVQLGLPRETARLLALQTAFGAAKLALESEE 222 ************************************************************************* PP TIGR00112 218 hpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 ++a+L+++Vts gGtT ++l+vLe +g+r+ +++a++aa +rs+eL NCBI__GCF_000378965.1:WP_018232723.1 223 DAATLRARVTSRGGTTEQALQVLESGGLRELLARALTAARDRSREL 268 *******************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (275 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: 16.66 // [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