Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_012408386.1 NPUN_RS08615 pyrroline-5-carboxylate reductase
Query= SwissProt::Q9HH99 (270 letters) >NCBI__GCF_000020025.1:WP_012408386.1 Length = 272 Score = 214 bits (546), Expect = 1e-60 Identities = 127/270 (47%), Positives = 168/270 (62%), Gaps = 6/270 (2%) Query: 5 KIGFIGAGKMGSALMQGTIKAGIVTPENIGASDVYEPFLKDLQAKLGIRVSTDNA-VIVR 63 K G IG G MG AL+ I GI + S+ L LQ + G+ V+TDN+ V + Sbjct: 4 KFGLIGGGVMGEALLSRLIARGIYQSSEVIVSEPLPSRLDFLQQQYGVSVTTDNSEVFTQ 63 Query: 64 ESDILILAVKPQTLSSVLSNLKN-EITSEK---LVISIAAGVPLSTYEDALLEGTRVVRV 119 +++ LAVKPQ S++ L + +I + + L+ISI AGVPL+ E A ++ V+R Sbjct: 64 AKEVVFLAVKPQVFSAIAQELADIDIINREQSPLIISILAGVPLNQLEAAFVQ-LPVIRA 122 Query: 120 MPNIAATVSEAASGIAPGKNATPEDLKAALEIFSAVGTAVQVPESLMDAVTGLSGSGPAF 179 MPN ATV + I G + + A ++FSAVG V+V E LMDAVTGLSGSGPA+ Sbjct: 123 MPNTPATVGAGITAICLGAYTNTKHHQIAQQVFSAVGEVVEVSEGLMDAVTGLSGSGPAY 182 Query: 180 IFPVIEAMADGAVLEGMDRKSALTLAAQTVLGAAKMALETGMHPGELKDMVTSPAGTTIQ 239 + ++E++ADG V G+ R A LA QTVLG AK+ ET MHP ELKD VTSP GTTI Sbjct: 183 VALLVESLADGGVSAGLPRAIANQLALQTVLGTAKLLYETKMHPAELKDRVTSPGGTTIA 242 Query: 240 GIHSLEEAGIRAAFMNAVIRASERSKELGK 269 GI LE+AG R+A + AV A+ERS+ELGK Sbjct: 243 GIAKLEQAGFRSALIEAVKAATERSQELGK 272 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: 187 Number of extensions: 9 Number of successful extensions: 4 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: 272 Length adjustment: 25 Effective length of query: 245 Effective length of database: 247 Effective search space: 60515 Effective search space used: 60515 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_012408386.1 NPUN_RS08615 (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.30852.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-96 306.9 3.7 8e-96 306.7 3.7 1.0 1 lcl|NCBI__GCF_000020025.1:WP_012408386.1 NPUN_RS08615 pyrroline-5-carboxy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020025.1:WP_012408386.1 NPUN_RS08615 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 306.7 3.7 8e-96 8e-96 2 263 .] 6 270 .. 5 270 .. 0.97 Alignments for each domain: == domain 1 score: 306.7 bits; conditional E-value: 8e-96 TIGR00112 2 aiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavk.eadvvllavKP 69 ++iG+G mgealls l+++g +++e++v e+ +++l+ l +++gv+vt+d+ e+ + +++vv+lavKP lcl|NCBI__GCF_000020025.1:WP_012408386.1 6 GLIGGGVMGEALLSRLIARGIYQSSEVIVSEPLPSRLDFLQQQYGVSVTTDNSEVFTqAKEVVFLAVKP 74 68************************************************99887651568******** PP TIGR00112 70 qdleevlaelks...eektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaasse 135 q+++++++el++ +++++ l+iSilAGv++++le ++ + +v+R+mPNt+a+vgag+tai+ +++ lcl|NCBI__GCF_000020025.1:WP_012408386.1 75 QVFSAIAQELADidiINREQSPLIISILAGVPLNQLEAAFV-QLPVIRAMPNTPATVGAGITAICLGAY 142 ***********999888999********************7.6************************** PP TIGR00112 136 vseeqkelveellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqt 204 ++ ++++ ++++++avG+vvev+e l+davt+lsGSgPA+v+ll+e+lad+gv +GLpr+ a++la qt lcl|NCBI__GCF_000020025.1:WP_012408386.1 143 TNTKHHQIAQQVFSAVGEVVEVSEGLMDAVTGLSGSGPAYVALLVESLADGGVSAGLPRAIANQLALQT 211 ********************************************************************* PP TIGR00112 205 lkGaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 + G+akll e++ hpa+Lkd+VtsPgGtTiag+a Le++g+rsa+ieav+aa++rs+eL lcl|NCBI__GCF_000020025.1:WP_012408386.1 212 VLGTAKLLYETKMHPAELKDRVTSPGGTTIAGIAKLEQAGFRSALIEAVKAATERSQEL 270 *********************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (272 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: 10.75 // [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