Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate WP_026608487.1 METAC_RS0120705 pyrroline-5-carboxylate reductase
Query= reanno::Caulo:CCNA_00528 (260 letters) >NCBI__GCF_000427445.1:WP_026608487.1 Length = 274 Score = 148 bits (374), Expect = 1e-40 Identities = 107/267 (40%), Positives = 145/267 (54%), Gaps = 15/267 (5%) Query: 4 ILLLGAGRMGGALIQGWQAAGAFDAADLIIRDPHVDA-----AAFAGAVVNPPLETLGAA 58 ++L GAG+MGGAL++ W G D + + DP AA G ++ P E Sbjct: 13 LVLAGAGKMGGALLRAWLDQG-IDPRRIAVLDPQPSPLIAALAAEKGFALDAPTEP---P 68 Query: 59 KTVLLAVKPQIWREAIADVVPHLAPDAVIVSIAAGVRAADISQAFG-GRRVARVMPTTAV 117 + ++LA+KPQ EA A + P ++VSI AG A+I+ F V R MP Sbjct: 69 EVLVLAIKPQSLDEAGA-LEPLAGAGTLVVSILAGKTIANIAARFPRAGAVVRAMPNLPA 127 Query: 118 AIGQGAASLYADDAEALAR---ARALFAPLAAVAELASEDLMHAATAVSGSAPAYLYAFI 174 A+G+G ++L D+ + A+ A AL L +E L+ A TAVSGS PAY++ Sbjct: 128 AVGRGISALCPSDSASPAQRALAEALIGAAGRFEWLPNERLIDAVTAVSGSGPAYVFYLT 187 Query: 175 EALEAAGAAQGLDPAQSARLARATIIGAAALMAQSGEE-PAELRKQVTSPGGTTAAALSV 233 E L AGAA GL SARLARAT+ G+ L+ +S + P ELR+ VTS GGTTAAAL V Sbjct: 188 ECLARAGAALGLPEDVSARLARATVEGSGELLFRSPDSTPTELRESVTSRGGTTAAALEV 247 Query: 234 LMGAGGFGDLLPKALDAAVARSKELGG 260 LM G L+ +A AA R + L G Sbjct: 248 LMAEDGLAPLIERAAAAARRRGEALSG 274 Lambda K H 0.318 0.131 0.366 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: 193 Number of extensions: 12 Number of successful extensions: 3 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: 260 Length of database: 274 Length adjustment: 25 Effective length of query: 235 Effective length of database: 249 Effective search space: 58515 Effective search space used: 58515 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_026608487.1 METAC_RS0120705 (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.28449.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-68 216.1 0.1 3.7e-68 216.0 0.1 1.0 1 lcl|NCBI__GCF_000427445.1:WP_026608487.1 METAC_RS0120705 pyrroline-5-carb Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000427445.1:WP_026608487.1 METAC_RS0120705 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 216.0 0.1 3.7e-68 3.7e-68 2 262 .. 14 271 .. 13 272 .. 0.94 Alignments for each domain: == domain 1 score: 216.0 bits; conditional E-value: 3.7e-68 TIGR00112 2 aiiGaGnmgeallsgllkkgakakkeilviers.eeklaalakelgvevtsdaeeavkeadvvllavKP 69 ++ GaG+mg all+++l +g ++ +i v +++ ++ +aala+e g + ++ + +v++la+KP lcl|NCBI__GCF_000427445.1:WP_026608487.1 14 VLAGAGKMGGALLRAWLDQGI-DPRRIAVLDPQpSPLIAALAAEKGFALDAPT----EPPEVLVLAIKP 77 678***************965.59*********8899999*****99999995....5778******** PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 q l+e+ a l+ + +++l++SilAG ti+++ ++ +vvR+mPN++a+vg+g++a++ s+ +s+ lcl|NCBI__GCF_000427445.1:WP_026608487.1 78 QSLDEAGA-LEP-LAGAGTLVVSILAGKTIANIAARFPRAGAVVRAMPNLPAAVGRGISALCPSDSASP 144 *****987.666.56699*************************************************** PP TIGR00112 139 eqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206 +q++l+e+l+ a G +++ e+l+davta+sGSgPA+vf+l e+la+ag +lGLp++ + +la++t++ lcl|NCBI__GCF_000427445.1:WP_026608487.1 145 AQRALAEALIGAAGRFEWLPnERLIDAVTAVSGSGPAYVFYLTECLARAGAALGLPEDVSARLARATVE 213 ********************************************************************* PP TIGR00112 207 Gaaklleesge.hpalLkdkVtsPgGtTiaglavLeekg.vrsavieaveaavkrsee 262 G+++ll +s + +p +L++ Vts gGtT+a+l+vL++++ + +++a aa +r e lcl|NCBI__GCF_000427445.1:WP_026608487.1 214 GSGELLFRSPDsTPTELRESVTSRGGTTAAALEVLMAEDgLAPLIERAAAAARRRGEA 271 ******999777**********************987654999999999999999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (274 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: 00:00:00.00 # Mc/sec: 7.40 // [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