Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_073039060.1 BUB04_RS10375 pyrroline-5-carboxylate reductase
Query= SwissProt::Q9HH99 (270 letters) >NCBI__GCF_900129305.1:WP_073039060.1 Length = 270 Score = 249 bits (637), Expect = 3e-71 Identities = 134/263 (50%), Positives = 176/263 (66%) Query: 6 IGFIGAGKMGSALMQGTIKAGIVTPENIGASDVYEPFLKDLQAKLGIRVSTDNAVIVRES 65 +GFIG G MG AL++G ++AGIV E + DV +K LQA G+ + A + + Sbjct: 7 VGFIGGGNMGEALIRGVLQAGIVPAERVVVFDVSRERMKHLQAAYGVVGAETLAACAQAA 66 Query: 66 DILILAVKPQTLSSVLSNLKNEITSEKLVISIAAGVPLSTYEDALLEGTRVVRVMPNIAA 125 +L+LAVKPQ ++ VL++L + + L+ISIAAGVPL T EDAL G VVRVMPN A Sbjct: 67 RVLVLAVKPQNMAGVLNDLADCVAHRPLIISIAAGVPLRTMEDALPPGVPVVRVMPNTPA 126 Query: 126 TVSEAASGIAPGKNATPEDLKAALEIFSAVGTAVQVPESLMDAVTGLSGSGPAFIFPVIE 185 V + AS +A G++A ++AAL +F AVG A ++ E L+DAVTGL+GSGPA++ +E Sbjct: 127 LVLQGASALARGRHADDTHMEAALTLFRAVGIAHELDEKLLDAVTGLTGSGPAYVLHFVE 186 Query: 186 AMADGAVLEGMDRKSALTLAAQTVLGAAKMALETGMHPGELKDMVTSPAGTTIQGIHSLE 245 ++ DG VL G+ R A L QTVLG A+M ETG HP ELKDMVTSP GTTI G+ LE Sbjct: 187 SLIDGGVLMGIPRPVARDLVVQTVLGTARMVQETGRHPSELKDMVTSPGGTTIHGLEVLE 246 Query: 246 EAGIRAAFMNAVIRASERSKELG 268 + G+R A M AV A+ERSK LG Sbjct: 247 KRGVRGAVMGAVRAATERSKALG 269 Lambda K H 0.313 0.130 0.343 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: 206 Number of extensions: 6 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: 270 Length of database: 270 Length adjustment: 25 Effective length of query: 245 Effective length of database: 245 Effective search space: 60025 Effective search space used: 60025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_073039060.1 BUB04_RS10375 (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.28246.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-90 289.5 1.1 1.5e-90 289.3 1.1 1.0 1 lcl|NCBI__GCF_900129305.1:WP_073039060.1 BUB04_RS10375 pyrroline-5-carbox Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900129305.1:WP_073039060.1 BUB04_RS10375 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 289.3 1.1 1.5e-90 1.5e-90 1 263 [] 7 268 .. 7 268 .. 0.99 Alignments for each domain: == domain 1 score: 289.3 bits; conditional E-value: 1.5e-90 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 +++iG+Gnmgeal++g+l++g +++++v + s e++++l +++gv +++ ++++++a v++lavKP lcl|NCBI__GCF_900129305.1:WP_073039060.1 7 VGFIGGGNMGEALIRGVLQAGIVPAERVVVFDVSRERMKHLQAAYGVVGAETLAACAQAARVLVLAVKP 75 68******************************************************************* PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 q++ vl++l++ ++ l+iSi+AGv++ ++e++l+ +vvRvmPNt+a v +g++a+a ++++++ lcl|NCBI__GCF_900129305.1:WP_073039060.1 76 QNMAGVLNDLAD-CVAHRPLIISIAAGVPLRTMEDALPPGVPVVRVMPNTPALVLQGASALARGRHADD 143 ***********9.66689*************************************************** PP TIGR00112 139 eqkelveellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkG 207 ++ e + l++avG ++e++eklldavt+l+GSgPA+v++++e+l+d+gv +G+pr a++l+ qt+ G lcl|NCBI__GCF_900129305.1:WP_073039060.1 144 THMEAALTLFRAVGIAHELDEKLLDAVTGLTGSGPAYVLHFVESLIDGGVLMGIPRPVARDLVVQTVLG 212 ********************************************************************* PP TIGR00112 208 aaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 +a++++e+g hp++Lkd VtsPgGtTi+gl+vLe+ gvr+av+ av+aa++rs+ L lcl|NCBI__GCF_900129305.1:WP_073039060.1 213 TARMVQETGRHPSELKDMVTSPGGTTIHGLEVLEKRGVRGAVMGAVRAATERSKAL 268 *****************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (270 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: 6.15 // [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