Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_011023994.1 MA_RS21405 pyrroline-5-carboxylate reductase
Query= SwissProt::Q9HH99 (270 letters) >NCBI__GCF_000007345.1:WP_011023994.1 Length = 270 Score = 508 bits (1307), Expect = e-149 Identities = 270/270 (100%), Positives = 270/270 (100%) Query: 1 MENQKIGFIGAGKMGSALMQGTIKAGIVTPENIGASDVYEPFLKDLQAKLGIRVSTDNAV 60 MENQKIGFIGAGKMGSALMQGTIKAGIVTPENIGASDVYEPFLKDLQAKLGIRVSTDNAV Sbjct: 1 MENQKIGFIGAGKMGSALMQGTIKAGIVTPENIGASDVYEPFLKDLQAKLGIRVSTDNAV 60 Query: 61 IVRESDILILAVKPQTLSSVLSNLKNEITSEKLVISIAAGVPLSTYEDALLEGTRVVRVM 120 IVRESDILILAVKPQTLSSVLSNLKNEITSEKLVISIAAGVPLSTYEDALLEGTRVVRVM Sbjct: 61 IVRESDILILAVKPQTLSSVLSNLKNEITSEKLVISIAAGVPLSTYEDALLEGTRVVRVM 120 Query: 121 PNIAATVSEAASGIAPGKNATPEDLKAALEIFSAVGTAVQVPESLMDAVTGLSGSGPAFI 180 PNIAATVSEAASGIAPGKNATPEDLKAALEIFSAVGTAVQVPESLMDAVTGLSGSGPAFI Sbjct: 121 PNIAATVSEAASGIAPGKNATPEDLKAALEIFSAVGTAVQVPESLMDAVTGLSGSGPAFI 180 Query: 181 FPVIEAMADGAVLEGMDRKSALTLAAQTVLGAAKMALETGMHPGELKDMVTSPAGTTIQG 240 FPVIEAMADGAVLEGMDRKSALTLAAQTVLGAAKMALETGMHPGELKDMVTSPAGTTIQG Sbjct: 181 FPVIEAMADGAVLEGMDRKSALTLAAQTVLGAAKMALETGMHPGELKDMVTSPAGTTIQG 240 Query: 241 IHSLEEAGIRAAFMNAVIRASERSKELGKK 270 IHSLEEAGIRAAFMNAVIRASERSKELGKK Sbjct: 241 IHSLEEAGIRAAFMNAVIRASERSKELGKK 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: 400 Number of extensions: 3 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_011023994.1 MA_RS21405 (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.29358.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-90 288.4 7.8 3.2e-90 288.3 7.8 1.0 1 lcl|NCBI__GCF_000007345.1:WP_011023994.1 MA_RS21405 pyrroline-5-carboxyla Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007345.1:WP_011023994.1 MA_RS21405 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 288.3 7.8 3.2e-90 3.2e-90 1 263 [] 6 267 .. 6 267 .. 0.99 Alignments for each domain: == domain 1 score: 288.3 bits; conditional E-value: 3.2e-90 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 i++iGaG+mg+al++g +k+g ++++i + e+ l++l ++lg++v++d++ +v+e+d+++lavKP lcl|NCBI__GCF_000007345.1:WP_011023994.1 6 IGFIGAGKMGSALMQGTIKAGIVTPENIGASDVYEPFLKDLQAKLGIRVSTDNAVIVRESDILILAVKP 74 89******************************99*********************************** PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 q l++vl++lk+ e t ekl+iSi+AGv+++++e++l + +rvvRvmPN+aa+v +++++ia ++++++ lcl|NCBI__GCF_000007345.1:WP_011023994.1 75 QTLSSVLSNLKN-EITSEKLVISIAAGVPLSTYEDALLEGTRVVRVMPNIAATVSEAASGIAPGKNATP 142 ***********9.8889*********************9****************************** PP TIGR00112 139 eqkelveellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkG 207 e+ + + e+++avG++v+v+e+l+davt+lsGSgPAf+f +iea+ad++v +G++r+ a++laaqt+ G lcl|NCBI__GCF_000007345.1:WP_011023994.1 143 EDLKAALEIFSAVGTAVQVPESLMDAVTGLSGSGPAFIFPVIEAMADGAVLEGMDRKSALTLAAQTVLG 211 ********************************************************************* PP TIGR00112 208 aaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 aak+ e+g hp +Lkd VtsP+GtTi+g+++Lee+g+r+a+++av +a++rs+eL lcl|NCBI__GCF_000007345.1:WP_011023994.1 212 AAKMALETGMHPGELKDMVTSPAGTTIQGIHSLEEAGIRAAFMNAVIRASERSKEL 267 ******************************************************98 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.72 // [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