Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate 3609259 Dshi_2645 pyrroline-5-carboxylate reductase (RefSeq)
Query= reanno::Caulo:CCNA_00528 (260 letters) >FitnessBrowser__Dino:3609259 Length = 273 Score = 166 bits (421), Expect = 4e-46 Identities = 112/264 (42%), Positives = 147/264 (55%), Gaps = 12/264 (4%) Query: 4 ILLLGAGRMGGALIQGWQAAGAFDAADLIIRDPH----VDAAAFAGAVVNPPLETLGAAK 59 + LLG G+MG A++QGW A G + ++ DP + A G +N + A Sbjct: 11 LFLLGCGKMGSAMLQGWLAQGIAPGSVWVL-DPKPSDWLTGLAAQGLHLNAGVPE--APA 67 Query: 60 TVLLAVKPQIWREAIADVVPHLAPDAVIVSIAAGVRAADISQAFG-GRRVARVMPTTAVA 118 LLAVKPQ+ +A+ V +++SIAAG AFG + R MP T A Sbjct: 68 IALLAVKPQMMGDALGPVTALGGGATLVLSIAAGTPIRFFEAAFGPATPIIRAMPNTPAA 127 Query: 119 IGQGAASLYADDAEA---LARARALFAPLAAVAELASEDLMHAATAVSGSAPAYLYAFIE 175 IG+G +L + A +A A AL + + L E M A TAVSGS PAY++ IE Sbjct: 128 IGKGITALVGNGAATEAHMALAEALLSAIGQTVRLEGEHQMDAVTAVSGSGPAYVFHLIE 187 Query: 176 ALEAAGAAQGLDPAQSARLARATIIGAAALMAQSGEEPAELRKQVTSPGGTTAAALSVLM 235 L AAG A+GL PA + +LA+AT+ GA AL + E PA+LR VTSPGGTTAAAL VLM Sbjct: 188 TLAAAGEAEGLPPALALQLAQATVAGAGALAEAADEGPAQLRVNVTSPGGTTAAALEVLM 247 Query: 236 GA-GGFGDLLPKALDAAVARSKEL 258 A GF LL +A+ AA R +EL Sbjct: 248 DAETGFPPLLRRAVAAAAQRGREL 271 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: 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: 260 Length of database: 273 Length adjustment: 25 Effective length of query: 235 Effective length of database: 248 Effective search space: 58280 Effective search space used: 58280 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 3609259 Dshi_2645 (pyrroline-5-carboxylate reductase (RefSeq))
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.4012.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-72 229.3 4.1 3.6e-72 229.1 4.1 1.0 1 lcl|FitnessBrowser__Dino:3609259 Dshi_2645 pyrroline-5-carboxylat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3609259 Dshi_2645 pyrroline-5-carboxylate reductase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 229.1 4.1 3.6e-72 3.6e-72 2 263 .] 12 271 .. 11 271 .. 0.93 Alignments for each domain: == domain 1 score: 229.1 bits; conditional E-value: 3.6e-72 TIGR00112 2 aiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevlae 78 ++G+G+mg+a+l+g+l++g + + +++v +++++ +++ g + ++ + ea + llavKPq++ ++l lcl|FitnessBrowser__Dino:3609259 12 FLLGCGKMGSAMLQGWLAQGIA-PGSVWVLDPKPSDWLTGLAAQGLHLNAGVPEAP---AIALLAVKPQMMGDALGP 84 589***************9765.9*******9977777777777788888866555...566**************9 PP TIGR00112 79 lkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellkavGkvv 155 ++ ++l++Si+AG++i +e +++ ++++R+mPNt+a++g+g+ta++ + +++e++ +l+e+ll+a+G++v lcl|FitnessBrowser__Dino:3609259 85 VTA-LGGGATLVLSIAAGTPIRFFEAAFGPATPIIRAMPNTPAAIGKGITALVGNGAATEAHMALAEALLSAIGQTV 160 888.66699******************************************************************** PP TIGR00112 156 eve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalLkdkVtsPgG 231 ++e e+++davta+sGSgPA+vf+lie la+ag ++GLp ++a++la++t++Ga++l e +e pa+L+ +VtsPgG lcl|FitnessBrowser__Dino:3609259 161 RLEgEHQMDAVTAVSGSGPAYVFHLIETLAAAGEAEGLPPALALQLAQATVAGAGALAEAADEGPAQLRVNVTSPGG 237 ***************************************************************************** PP TIGR00112 232 tTiaglavLeekg..vrsavieaveaavkrseeL 263 tT+a+l+vL++++ + + +av aa++r +eL lcl|FitnessBrowser__Dino:3609259 238 TTAAALEVLMDAEtgFPPLLRRAVAAAAQRGREL 271 *********9654349**************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (273 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: 8.08 // [ok]
This GapMind analysis is from Apr 09 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