Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate CCNA_00528 CCNA_00528 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__Caulo:CCNA_00528 Length = 260 Score = 150 bits (380), Expect = 2e-41 Identities = 105/264 (39%), Positives = 140/264 (53%), Gaps = 11/264 (4%) Query: 6 IAFIGAGNMAASLIGGLRAQGV-PAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADA 64 I +GAG M +LI G +A G AA + DP + A FA VV E + A Sbjct: 4 ILLLGAGRMGGALIQGWQAAGAFDAADLIIRDPHVD-----AAAFAGAVVNPPLETLGAA 58 Query: 65 DVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPA 124 V+L+VKPQ + + P L P+ +IVSIAAG+ A + G R V R MP T Sbjct: 59 KTVLLAVKPQIWREAIADVVPHLAPDAVIVSIAAGVRAADISQAFGGRR-VARVMPTTAV 117 Query: 125 LLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLM 184 + QGA+ LYA+ A +A L + + L E + A TAVSGS PAY + + Sbjct: 118 AIGQGAASLYAD---DAEALARARALFAPLAAVAELASEDLMHAATAVSGSAPAYLYAFI 174 Query: 185 QAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKSF 244 +A+ AG GL ++RL T +GAA + S EPAELR++VTSP GTT AA+ Sbjct: 175 EALEAAGAAQGLDPAQSARLARATIIGAAALMAQSGEEPAELRKQVTSPGGTTAAALSVL 234 Query: 245 Q-ANGFEALVEQALNAASQRSAEL 267 A GF L+ +AL+AA RS EL Sbjct: 235 MGAGGFGDLLPKALDAAVARSKEL 258 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: 172 Number of extensions: 10 Number of successful extensions: 5 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: 260 Length adjustment: 25 Effective length of query: 248 Effective length of database: 235 Effective search space: 58280 Effective search space used: 58280 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 CCNA_00528 CCNA_00528 (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.14579.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-73 232.2 9.0 4.8e-73 232.0 9.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_00528 CCNA_00528 pyrroline-5-carboxyla Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_00528 CCNA_00528 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 232.0 9.0 4.8e-73 4.8e-73 1 263 [] 4 258 .. 4 258 .. 0.91 Alignments for each domain: == domain 1 score: 232.0 bits; conditional E-value: 4.8e-73 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdle 73 i ++GaG+mg al++g++++ga +++++++ +++ ++ aa+ +g+ v+ + e +a++vllavKPq ++ lcl|FitnessBrowser__Caulo:CCNA_00528 4 ILLLGAGRMGGALIQGWQAAGAFDAADLIIRDPHVDA-AAF---AGAVVNPPL-ETLGAAKTVLLAVKPQIWR 71 679********************88888777644333.222...334445554.5566888************ PP TIGR00112 74 evlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelvee 146 e++a++ + + +++++Si+AGv++++++q++++ +rv+RvmP ta+++g+g+++++a+ ++e +++++ lcl|FitnessBrowser__Caulo:CCNA_00528 72 EAIADVVP-HLAPDAVIVSIAAGVRAADISQAFGG-RRVARVMPTTAVAIGQGAASLYAD---DAEALARARA 139 *****999.7779********************86.99*********************9...4567899*** PP TIGR00112 147 llkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgeh 218 l++ ++ v e++ e+l++a+ta+sGS+PA+++ +ieal++ag ++GL+ +++ +la++t++Gaa+l+++sge+ lcl|FitnessBrowser__Caulo:CCNA_00528 140 LFAPLAAVAELAsEDLMHAATAVSGSAPAYLYAFIEALEAAGAAQGLDPAQSARLARATIIGAAALMAQSGEE 212 ************************************************************************* PP TIGR00112 219 palLkdkVtsPgGtTiaglavLeekg.vrsavieaveaavkrseeL 263 pa+L+++VtsPgGtT+a+l+vL+ +g + + + +a++aav+rs+eL lcl|FitnessBrowser__Caulo:CCNA_00528 213 PAELRKQVTSPGGTTAAALSVLMGAGgFGDLLPKALDAAVARSKEL 258 **********************98766*****************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (260 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: 00:00:00.00 # Mc/sec: 10.69 // [ok]
This GapMind analysis is from Sep 17 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