Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate BPHYT_RS03490 BPHYT_RS03490 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__BFirm:BPHYT_RS03490 Length = 271 Score = 223 bits (567), Expect = 4e-63 Identities = 121/269 (44%), Positives = 165/269 (61%) Query: 5 RIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADA 64 +IAFIG GNMAA+LIGGL +GV A + A DP + + +F I + +A Sbjct: 2 KIAFIGGGNMAAALIGGLIKRGVAPADLYAIDPNEDALKRNEQQFGIKTGAAADAGLAAY 61 Query: 65 DVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPA 124 D VVL+VKPQ +K+V +A+AP L QL VSI AGI + WL +VR MPNTPA Sbjct: 62 DAVVLAVKPQILKSVAEAVAPHLNASQLAVSIVAGIRMGDMSRWLNGHDRIVRVMPNTPA 121 Query: 125 LLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLM 184 L+ G +GL A + V A A Q+L AVG +W DDEA+IDAVTA+SGSGPAY F + Sbjct: 122 LIGMGVTGLVATSSVDEAGRALASQVLGAVGETVWFDDEAKIDAVTAISGSGPAYVFYFI 181 Query: 185 QAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKSF 244 +A+ +A +LG+ L + T GAAQ+A +S+ P+ LR RVTS GTT AA+ SF Sbjct: 182 EALQEAARQLGMDESQGRALAVATFTGAAQLAANSDEPPSVLRERVTSKGGTTAAALASF 241 Query: 245 QANGFEALVEQALNAASQRSAELAEQLGQ 273 A+G + + + AA R+ E+ ++ G+ Sbjct: 242 DASGIKDAIVRGALAADARAKEMGDEFGK 270 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: 185 Number of extensions: 7 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: 271 Length adjustment: 25 Effective length of query: 248 Effective length of database: 246 Effective search space: 61008 Effective search space used: 61008 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 BPHYT_RS03490 BPHYT_RS03490 (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.8296.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-79 252.4 5.5 3.3e-79 252.2 5.5 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS03490 BPHYT_RS03490 pyrroline-5-carbox Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS03490 BPHYT_RS03490 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 252.2 5.5 3.3e-79 3.3e-79 1 263 [] 3 264 .. 3 264 .. 0.98 Alignments for each domain: == domain 1 score: 252.2 bits; conditional E-value: 3.3e-79 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPq 70 ia+iG+Gnm++al+ gl+k+g++ +++++ i+++e++l+++ +++g+++ ++a++ ++ d v+lavKPq lcl|FitnessBrowser__BFirm:BPHYT_RS03490 3 IAFIGGGNMAAALIGGLIKRGVA-PADLYAIDPNEDALKRNEQQFGIKTGAAADAGLAAYDAVVLAVKPQ 71 89*****************9887.9********************************************* PP TIGR00112 71 dleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeq 140 l++v++ ++ + ++++l +Si+AG+++ +++++l+++ r+vRvmPNt+a +g gvt+++a+s v+e+ lcl|FitnessBrowser__BFirm:BPHYT_RS03490 72 ILKSVAEAVAP-HLNASQLAVSIVAGIRMGDMSRWLNGHDRIVRVMPNTPALIGMGVTGLVATSSVDEAG 140 *******9998.77799***************************************************** PP TIGR00112 141 kelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaa 209 ++l++++l avG++v+ + e+++davta+sGSgPA+vf++ieal++a+ +lG+++++ ++la +t+ Gaa lcl|FitnessBrowser__BFirm:BPHYT_RS03490 141 RALASQVLGAVGETVWFDdEAKIDAVTAISGSGPAYVFYFIEALQEAARQLGMDESQGRALAVATFTGAA 210 ********************************************************************** PP TIGR00112 210 klleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 +l ++s+e p++L+++Vts+gGtT+a+la++ ++g+++a+ ++ aa +r++e+ lcl|FitnessBrowser__BFirm:BPHYT_RS03490 211 QLAANSDEPPSVLRERVTSKGGTTAAALASFDASGIKDAIVRGALAADARAKEM 264 **************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (271 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: 6.28 // [ok]
This GapMind analysis is from Apr 09 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