Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_011736668.1 PPRO_RS14015 pyrroline-5-carboxylate reductase
Query= SwissProt::Q9HH99 (270 letters) >NCBI__GCF_000015045.1:WP_011736668.1 Length = 270 Score = 238 bits (606), Expect = 1e-67 Identities = 131/268 (48%), Positives = 171/268 (63%), Gaps = 1/268 (0%) Query: 3 NQKIGFIGAGKMGSALMQGTIKAGIVTPENIGASDVYEPFLKDLQAKLGIRVSTDNAVIV 62 N+KIGFIG G M A+++G + A + I ++ E K L + GI S + + Sbjct: 4 NKKIGFIGGGNMAEAIIKGLL-ADSFRADAIMVAEPQEQRRKSLSSTYGIGTSDSGSAVA 62 Query: 63 RESDILILAVKPQTLSSVLSNLKNEITSEKLVISIAAGVPLSTYEDALLEGTRVVRVMPN 122 ++DI+ILA+KPQ + VLS+L+ I ++KLVISI AG+P + E++L G RVVRVMPN Sbjct: 63 GQADIVILAIKPQMAAGVLSDLEPAIPADKLVISIMAGIPTTYIEESLASGVRVVRVMPN 122 Query: 123 IAATVSEAASGIAPGKNATPEDLKAALEIFSAVGTAVQVPESLMDAVTGLSGSGPAFIFP 182 AA + AAS I PG+ A DL A EIFS VG V E LMDAVTGLSGSGPA++F Sbjct: 123 TAALIQAAASAICPGRKADDSDLATATEIFSRVGAVVTTTEKLMDAVTGLSGSGPAYVFS 182 Query: 183 VIEAMADGAVLEGMDRKSALTLAAQTVLGAAKMALETGMHPGELKDMVTSPAGTTIQGIH 242 IEA++D V G+ R +L LA QTVLGAA+M ETG HP L++ VTSP GTTI G+H Sbjct: 183 FIEALSDAGVKNGLARDVSLKLAVQTVLGAARMVDETGDHPALLREKVTSPGGTTIAGLH 242 Query: 243 SLEEAGIRAAFMNAVIRASERSKELGKK 270 +LE M+AV A +S+EL K Sbjct: 243 TLENGRFHGLVMDAVDSACAKSRELAGK 270 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: 214 Number of extensions: 3 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: 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_011736668.1 PPRO_RS14015 (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.15938.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-93 298.9 3.6 2.1e-93 298.7 3.6 1.0 1 lcl|NCBI__GCF_000015045.1:WP_011736668.1 PPRO_RS14015 pyrroline-5-carboxy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011736668.1 PPRO_RS14015 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 298.7 3.6 2.1e-93 2.1e-93 1 263 [] 7 267 .. 7 267 .. 0.99 Alignments for each domain: == domain 1 score: 298.7 bits; conditional E-value: 2.1e-93 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 i++iG+Gnm+ea+++gll+ + + ++ i+v+e++e++++ l ++g+ ++ + +++ +ad+v+la+KP lcl|NCBI__GCF_000015045.1:WP_011736668.1 7 IGFIGGGNMAEAIIKGLLADSFR-ADAIMVAEPQEQRRKSLSSTYGIGTSDSGSAVAGQADIVILAIKP 74 89*****************9777.89******************************************* PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 q++ vl++l+ ++kl+iSi+AG+++ ++e+ l++ rvvRvmPNtaa ++a+++ai+ ++++++ lcl|NCBI__GCF_000015045.1:WP_011736668.1 75 QMAAGVLSDLEP-AIPADKLVISIMAGIPTTYIEESLASGVRVVRVMPNTAALIQAAASAICPGRKADD 142 ***********9.8889**************************************************** PP TIGR00112 139 eqkelveellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkG 207 ++ ++++e++++vG vv+ +ekl+davt+lsGSgPA+vf +ieal dagvk+GL r+ +++la qt+ G lcl|NCBI__GCF_000015045.1:WP_011736668.1 143 SDLATATEIFSRVGAVVTTTEKLMDAVTGLSGSGPAYVFSFIEALSDAGVKNGLARDVSLKLAVQTVLG 211 ********************************************************************* PP TIGR00112 208 aaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 aa+++ e+g+hpalL++kVtsPgGtTiagl++Le++++ + v++av++a ++s+eL lcl|NCBI__GCF_000015045.1:WP_011736668.1 212 AARMVDETGDHPALLREKVTSPGGTTIAGLHTLENGRFHGLVMDAVDSACAKSREL 267 *****************************************************998 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.97 // [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