Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate Echvi_2479 Echvi_2479 pyrroline-5-carboxylate reductase
Query= reanno::Pedo557:CA265_RS18505 (269 letters) >FitnessBrowser__Cola:Echvi_2479 Length = 265 Score = 231 bits (589), Expect = 1e-65 Identities = 117/255 (45%), Positives = 170/255 (66%) Query: 3 KIAIIGSGNIGLSLAKGLVKANYTTTKNIILTRRNTANLYKFAQERYKVTANNADAAADA 62 KIAIIG GN+GLS+ GL++ KN+++T+R+ NL VTA+N AA A Sbjct: 5 KIAIIGCGNLGLSIVNGLLETEGFEAKNLMVTKRHPENLSHLQSLGVTVTADNKSAAKAA 64 Query: 63 DVIILAVLPQQLNVVLEEIQSAINPAKHLVISVISGVSCAAVREKLDSNVQIIRAMPNTA 122 D++IL V P + +L+EI ++P K +IS+ +GV+ + + L S + RAMPN A Sbjct: 65 DLVILGVKPYNIPHILKEIAPVVSPDKQTIISLATGVTLEEMYQHLPSTTALYRAMPNIA 124 Query: 123 IAIGQSMTCIASDNASPQNLEDVTRMFETVGSVVKINEDLMTSATALCACGIAFFLRGIR 182 I +S+TCI N++P+N + + +F ++G + I E LM +AT L ACGIA+ LR +R Sbjct: 125 ADIQESITCICGQNSTPENEDIIKALFNSIGISIIIEEHLMEAATVLGACGIAYVLRFMR 184 Query: 183 AASQGGVEIGFHADEALKMAVQTAKGAADLLLLHGTHPESEIDKVTSPKGCTIAGLNEME 242 A +QGG++IGF A A + QT KGAA+LL+ G HPE+ IDKVT+PKGCTI GLNEME Sbjct: 185 AMTQGGIQIGFDAKTANTIVNQTVKGAAELLIKKGIHPEAAIDKVTTPKGCTIVGLNEME 244 Query: 243 HNGYSSSLIKGIKLS 257 H+G+S++++KG+ S Sbjct: 245 HHGFSAAMVKGVLAS 259 Lambda K H 0.316 0.130 0.355 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: 202 Number of extensions: 7 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: 269 Length of database: 265 Length adjustment: 25 Effective length of query: 244 Effective length of database: 240 Effective search space: 58560 Effective search space used: 58560 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 (21.6 bits) S2: 47 (22.7 bits)
Align candidate Echvi_2479 Echvi_2479 (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.29018.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-73 231.1 4.1 1e-72 230.9 4.1 1.0 1 lcl|FitnessBrowser__Cola:Echvi_2479 Echvi_2479 pyrroline-5-carboxyla Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2479 Echvi_2479 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 230.9 4.1 1e-72 1e-72 1 260 [. 6 263 .. 6 265 .] 0.97 Alignments for each domain: == domain 1 score: 230.9 bits; conditional E-value: 1e-72 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdlee 74 iaiiG+Gn+g ++++gll+++ ++k+++v++r++e+l ++++lgv+vt+d+++a+k+ad+v+l+vKP+++++ lcl|FitnessBrowser__Cola:Echvi_2479 6 IAIIGCGNLGLSIVNGLLETEGFEAKNLMVTKRHPENLS-HLQSLGVTVTADNKSAAKAADLVILGVKPYNIPH 78 89*********************999**99999988876.6799****************************** PP TIGR00112 75 vlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveell 148 +l+e++ + ++++iS++ Gvt+e+++q+l+++++++R+mPN+aa +++++t i+ + + ++e+++ +++l+ lcl|FitnessBrowser__Cola:Echvi_2479 79 ILKEIAPVVSPDKQTIISLATGVTLEEMYQHLPSTTALYRAMPNIAADIQESITCICGQ-NSTPENEDIIKALF 151 *******99999**********************************************9.5779999******* PP TIGR00112 149 kavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalL 222 +++G + +ee+l++a+t l ++g A+v+ ++ a+ ++g++ G+++++a++++ qt+kGaa+ll ++g hp++ lcl|FitnessBrowser__Cola:Echvi_2479 152 NSIGISIIIEEHLMEAATVLGACGIAYVLRFMRAMTQGGIQIGFDAKTANTIVNQTVKGAAELLIKKGIHPEAA 225 ************************************************************************** PP TIGR00112 223 kdkVtsPgGtTiaglavLeekgvrsavieaveaavkrs 260 +dkVt+P+G+Ti gl+++e++g+ +a+ ++v a++++ lcl|FitnessBrowser__Cola:Echvi_2479 226 IDKVTTPKGCTIVGLNEMEHHGFSAAMVKGVLASYEKI 263 **********************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (265 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: 10.50 // [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