Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_015739027.1 ADEG_RS05155 pyrroline-5-carboxylate reductase
Query= SwissProt::Q9HH99 (270 letters) >NCBI__GCF_000024605.1:WP_015739027.1 Length = 282 Score = 234 bits (596), Expect = 2e-66 Identities = 130/264 (49%), Positives = 173/264 (65%), Gaps = 1/264 (0%) Query: 5 KIGFIGAGKMGSALMQGTIKAGIVTPENIGASDVYEPFLKDLQAKLGIRVSTDNAVIVRE 64 K+GFIG G MG AL G +++G V PE + SDV L +L LGI+ +DN + +E Sbjct: 8 KVGFIGGGAMGGALATGLVRSGRVAPEQVLVSDVSAERLAELSRTLGIKTLSDNRSLAQE 67 Query: 65 SDILILAVKPQTLSSVLSNLKNEITSEKLVISIAAGVPLSTYEDALLEGTRVVRVMPNIA 124 +DI++LAVKP + VL + + + E+ +ISIAAGV L+ + + VVRVMPN Sbjct: 68 ADIIVLAVKPDQVRPVLEEISDLVRPEQTLISIAAGVSLAELQSWAGKAVPVVRVMPNTP 127 Query: 125 ATVSEAASGIAPGKNATPEDLKAALEIFSAVGTAVQVP-ESLMDAVTGLSGSGPAFIFPV 183 A V E AS A G +A D + + SAVG V+VP E L+DAVTGLSGSGPA+++ V Sbjct: 128 ALVGEGASAYALGSHAGSRDAERTEALMSAVGRVVRVPKEELLDAVTGLSGSGPAYVYLV 187 Query: 184 IEAMADGAVLEGMDRKSALTLAAQTVLGAAKMALETGMHPGELKDMVTSPAGTTIQGIHS 243 IEA+A+G V G+ K AL LAAQTVLGAAKM L + HP LK V +PAGTT++G+ Sbjct: 188 IEALAEGGVRMGLSWKEALLLAAQTVLGAAKMVLASEEHPSVLKGRVMTPAGTTVEGLFV 247 Query: 244 LEEAGIRAAFMNAVIRASERSKEL 267 LE+ G+RAAF+ AV A+ RSKE+ Sbjct: 248 LEDRGVRAAFIEAVKAAALRSKEM 271 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: 237 Number of extensions: 7 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: 282 Length adjustment: 25 Effective length of query: 245 Effective length of database: 257 Effective search space: 62965 Effective search space used: 62965 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_015739027.1 ADEG_RS05155 (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.16983.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-92 294.0 3.8 6.7e-92 293.8 3.8 1.0 1 lcl|NCBI__GCF_000024605.1:WP_015739027.1 ADEG_RS05155 pyrroline-5-carboxy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024605.1:WP_015739027.1 ADEG_RS05155 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 293.8 3.8 6.7e-92 6.7e-92 1 263 [] 9 271 .. 9 271 .. 0.99 Alignments for each domain: == domain 1 score: 293.8 bits; conditional E-value: 6.7e-92 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 +++iG+G mg al++gl+++g+ a++++lv + s+e+la+l +lg+++ sd++++++ead+++lavKP lcl|NCBI__GCF_000024605.1:WP_015739027.1 9 VGFIGGGAMGGALATGLVRSGRVAPEQVLVSDVSAERLAELSRTLGIKTLSDNRSLAQEADIIVLAVKP 77 68******************************************************************* PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 ++++vl+e+ + + e++liSi+AGv++++l++++++ +vvRvmPNt+a vg+g++a+a +s++ + lcl|NCBI__GCF_000024605.1:WP_015739027.1 78 DQVRPVLEEISD-LVRPEQTLISIAAGVSLAELQSWAGKAVPVVRVMPNTPALVGEGASAYALGSHAGS 145 ********9998.7779**************************************************** PP TIGR00112 139 eqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206 + e+ e+l++avG vv+v+ e+lldavt+lsGSgPA+v+l+ieala++gv++GL+ +ea+ laaqt+ lcl|NCBI__GCF_000024605.1:WP_015739027.1 146 RDAERTEALMSAVGRVVRVPkEELLDAVTGLSGSGPAYVYLVIEALAEGGVRMGLSWKEALLLAAQTVL 214 ********************************************************************* PP TIGR00112 207 GaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 Gaak++ s+ehp++Lk +V++P+GtT++gl vLe+ gvr+a+ieav+aa+ rs+e+ lcl|NCBI__GCF_000024605.1:WP_015739027.1 215 GAAKMVLASEEHPSVLKGRVMTPAGTTVEGLFVLEDRGVRAAFIEAVKAAALRSKEM 271 ******************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (282 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: 10.32 // [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