Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_053938794.1 WG78_RS15740 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_001294205.1:WP_053938794.1 Length = 272 Score = 212 bits (539), Expect = 8e-60 Identities = 117/269 (43%), Positives = 169/269 (62%), Gaps = 2/269 (0%) Query: 5 RIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADA 64 +I FIG GNMA +LIGG+ QG A Q+ +P A +R ++ EF + V +A A + Sbjct: 2 KITFIGGGNMAGALIGGMTQQGFSADQLHVVEPDAARRDQLVEEFGVSVSAPDAPRPA-S 60 Query: 65 DVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPA 124 DVV+ +VKPQ ++ V QA A + L++SIAAG+ ++ WL R +VR MPNTPA Sbjct: 61 DVVIFAVKPQQLRPVVQA-ALQNGDQPLLISIAAGVRAETISRWLDGYRRIVRVMPNTPA 119 Query: 125 LLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLM 184 L+R G SGLYA +V+A + ++ +++G +WLD+E+QID +TA+SGSGPAY F M Sbjct: 120 LVRAGMSGLYAAPEVNAEDRALSERIFTSIGKTVWLDEESQIDGLTAISGSGPAYVFYFM 179 Query: 185 QAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKSF 244 +A+ A G S + A L QT G+ ++AL S+ + A LR +VTS GTTE AI +F Sbjct: 180 EALQAAARAQGFSPDVAHLLAYQTVAGSVKLALESDDDAATLRVKVTSKGGTTERAINAF 239 Query: 245 QANGFEALVEQALNAASQRSAELAEQLGQ 273 + + A + A AA+ RS EL E+LG+ Sbjct: 240 ENSQMRATIIAAAAAAAARSRELGEELGR 268 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: 9 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: 272 Length adjustment: 25 Effective length of query: 248 Effective length of database: 247 Effective search space: 61256 Effective search space used: 61256 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_053938794.1 WG78_RS15740 (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.carbon/TIGR00112.hmm # target sequence database: /tmp/gapView.3021522.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-82 261.1 0.7 7.4e-82 260.9 0.7 1.0 1 NCBI__GCF_001294205.1:WP_053938794.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001294205.1:WP_053938794.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.9 0.7 7.4e-82 7.4e-82 1 263 [] 3 262 .. 3 262 .. 0.97 Alignments for each domain: == domain 1 score: 260.9 bits; conditional E-value: 7.4e-82 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdle 73 i++iG+Gnm+ al+ g+ ++g + +++++v+e+ ++++++l++e+gv+v++++ + ++dvv++avKPq+l+ NCBI__GCF_001294205.1:WP_053938794.1 3 ITFIGGGNMAGALIGGMTQQGFS-ADQLHVVEPDAARRDQLVEEFGVSVSAPD-APRPASDVVIFAVKPQQLR 73 79*****************9887.8*************************995.6777999************ PP TIGR00112 74 evlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelvee 146 +v++ + + + lliSi+AGv++e+++++l++ +r+vRvmPNt+a v+ag+++++a ev++e+++l e+ NCBI__GCF_001294205.1:WP_053938794.1 74 PVVQAALQ--NGDQPLLISIAAGVRAETISRWLDGYRRIVRVMPNTPALVRAGMSGLYAAPEVNAEDRALSER 144 ***96555..5579*********************************************************** PP TIGR00112 147 llkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgeh 218 +++++Gk+v+++ e+++d +ta+sGSgPA+vf+++eal++a+ ++G++ + a la+qt++G++kl es+++ NCBI__GCF_001294205.1:WP_053938794.1 145 IFTSIGKTVWLDeESQIDGLTAISGSGPAYVFYFMEALQAAARAQGFSPDVAHLLAYQTVAGSVKLALESDDD 217 ************99*********************************************************** PP TIGR00112 219 palLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 +a+L+ kVts+gGtT ++++++e++++r+++i+a aa++rs+eL NCBI__GCF_001294205.1:WP_053938794.1 218 AATLRVKVTSKGGTTERAINAFENSQMRATIIAAAAAAAARSREL 262 ******************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (272 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: 21.23 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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