Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_044411124.1 NA59_RS08760 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_000934765.1:WP_044411124.1 Length = 273 Score = 279 bits (714), Expect = 4e-80 Identities = 145/269 (53%), Positives = 193/269 (71%), Gaps = 1/269 (0%) Query: 6 IAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADAD 65 I FIGAGNM+ SLIGGL G P QI ASDP ++ A + + I+ E N A+ AD Sbjct: 5 ICFIGAGNMSRSLIGGLIQSGYPKNQIWASDPSSQALAALKQNYGIEGFEDNLTAIDKAD 64 Query: 66 VVVLSVKPQAMKAVCQALAPALKPE-QLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPA 124 ++VL+VKPQ +KA+CQ +A LK +LI+S+AAGI S++ WLG + +VR MPNTPA Sbjct: 65 IIVLAVKPQQLKALCQTMAEPLKTSSKLIISVAAGIKTQSIDHWLGGHQSIVRTMPNTPA 124 Query: 125 LLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLM 184 L++ GA+GL+AN VS Q + A +L A G+ +W+D+E ++DAVTA+SGSGPAYFFL M Sbjct: 125 LIQTGATGLFANHHVSQQQKDDAENILRAAGLTIWVDNEDKLDAVTALSGSGPAYFFLFM 184 Query: 185 QAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKSF 244 +AM AGEKLGL +TA LT+QTA GAA+MAL S ELRR VTSPNGTTE AI+SF Sbjct: 185 EAMQAAGEKLGLDAKTAELLTMQTAFGAAKMALESHESCNELRRMVTSPNGTTERAIQSF 244 Query: 245 QANGFEALVEQALNAASQRSAELAEQLGQ 273 + G ++V+ A+ AA QR+ +LA++LG+ Sbjct: 245 EQAGLASVVDNAMQAAHQRAQQLAQELGE 273 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: 8 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: 273 Length adjustment: 25 Effective length of query: 248 Effective length of database: 248 Effective search space: 61504 Effective search space used: 61504 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_044411124.1 NA59_RS08760 (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.16746.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-85 273.0 2.4 1.7e-85 272.8 2.4 1.0 1 lcl|NCBI__GCF_000934765.1:WP_044411124.1 NA59_RS08760 pyrroline-5-carboxy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000934765.1:WP_044411124.1 NA59_RS08760 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 272.8 2.4 1.7e-85 1.7e-85 1 263 [] 5 267 .. 5 267 .. 0.99 Alignments for each domain: == domain 1 score: 272.8 bits; conditional E-value: 1.7e-85 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 i +iGaGnm ++l+ gl+++g + k++i+ ++s+++laal +++g+e +d+ +a+++ad+++lavKP lcl|NCBI__GCF_000934765.1:WP_044411124.1 5 ICFIGAGNMSRSLIGGLIQSGYP-KNQIWASDPSSQALAALKQNYGIEGFEDNLTAIDKADIIVLAVKP 72 68******************887.8******************************************** PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 q+l+++++++++ kt +kl+iS++AG++++ + ++l++++ +vR mPNt+a ++ g+t+++a+++vs+ lcl|NCBI__GCF_000934765.1:WP_044411124.1 73 QQLKALCQTMAEPLKTSSKLIISVAAGIKTQSIDHWLGGHQSIVRTMPNTPALIQTGATGLFANHHVSQ 141 ************9999***************************************************** PP TIGR00112 139 eqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206 +qk+ +e++l+a G +++v+ e++ldavtalsGSgPA++fl++ea+++ag klGL++++a+ l++qt lcl|NCBI__GCF_000934765.1:WP_044411124.1 142 QQKDDAENILRAAGLTIWVDnEDKLDAVTALSGSGPAYFFLFMEAMQAAGEKLGLDAKTAELLTMQTAF 210 ********************************************************************* PP TIGR00112 207 GaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 Gaak+ es+e+ ++L+ VtsP+GtT ++++++e++g+ s v++a++aa +r+++L lcl|NCBI__GCF_000934765.1:WP_044411124.1 211 GAAKMALESHESCNELRRMVTSPNGTTERAIQSFEQAGLASVVDNAMQAAHQRAQQL 267 *******************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (273 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: 8.24 // [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