Align Pyrroline-5-carboxylate reductase 1; P5C reductase 1; P5CR 1; EC 1.5.1.2; PCA reductase 1 (uncharacterized)
to candidate WP_015944064.1 DHAF_RS12400 pyrroline-5-carboxylate reductase
Query= curated2:E0TY11 (297 letters) >NCBI__GCF_000021925.1:WP_015944064.1 Length = 267 Score = 185 bits (470), Expect = 8e-52 Identities = 100/263 (38%), Positives = 164/263 (62%), Gaps = 5/263 (1%) Query: 17 KKVAFIGAGSMAEGMISGIVRANKIPKQNICVTNRSNTERLAELELQYGIKGASPNQICI 76 KK++FIGAG+MAE +I G++ I VTNRSN +LA+++ YG+ S + + Sbjct: 2 KKISFIGAGNMAEAIIKGLMVTGSY---EIRVTNRSNQAKLAQMKEDYGVIPVSFRE-AV 57 Query: 77 EDMDVLILAMKPKDAESALSSLKTRIQPHQLILSVLAGITTSFIEQSLLNQQPVVRVMPN 136 +D ++++LA+KPKD AL+ ++ I +QL++SV AGI + +E+ L + P++R MPN Sbjct: 58 KDSEIILLAVKPKDVGEALAQIREGISSNQLLISVAAGIPLALLEKHLPHC-PIIRAMPN 116 Query: 137 TSSMIGASATAIALGKYVSEDLQKLAEALLGCMGEVYTIQENQMDIFTGIAGSGPAYFYY 196 TSS + S T + G+ V+E Q+ E + G +G+ I E Q++ ++GSGPAYFY Sbjct: 117 TSSAVLHSMTGLVKGQGVNEAKQRDVEDIFGAVGKYIWITEEQINPLIAMSGSGPAYFYL 176 Query: 197 LMEFIEKTGEEAGLDKQLSRSIGAQTLLGAAKMLMETGEQPEVLRDNITSPNGTTAAGLQ 256 E + K G + G ++++ ++ +TL+GAAKML ++G+ P LR +TSP GTT L+ Sbjct: 177 FTEALVKAGVDMGFSQEVAENLAKETLMGAAKMLAQSGKSPGELRVAVTSPKGTTQEALE 236 Query: 257 ALKKSGGGEAISQAIKHAAKRSK 279 ++ G E ++QA K R++ Sbjct: 237 VFREQGLEELVAQAAKACKHRAQ 259 Lambda K H 0.314 0.130 0.349 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: 11 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: 297 Length of database: 267 Length adjustment: 26 Effective length of query: 271 Effective length of database: 241 Effective search space: 65311 Effective search space used: 65311 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 (22.0 bits) S2: 47 (22.7 bits)
Align candidate WP_015944064.1 DHAF_RS12400 (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.27875.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-82 263.6 4.6 1.2e-82 263.4 4.6 1.0 1 lcl|NCBI__GCF_000021925.1:WP_015944064.1 DHAF_RS12400 pyrroline-5-carboxy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021925.1:WP_015944064.1 DHAF_RS12400 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 263.4 4.6 1.2e-82 1.2e-82 1 262 [. 4 260 .. 4 261 .. 0.96 Alignments for each domain: == domain 1 score: 263.4 bits; conditional E-value: 1.2e-82 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilviers.eeklaalakelgvevtsdaeeavkeadvvllavK 68 i++iGaGnm+ea+++gl+ +g +ei v++rs ++kla++ +++gv +s +eavk+++++llavK lcl|NCBI__GCF_000021925.1:WP_015944064.1 4 ISFIGAGNMAEAIIKGLMVTGS---YEIRVTNRSnQAKLAQMKEDYGVIPVSF-REAVKDSEIILLAVK 68 79***************99854...69*******8889999999999888887.6899*********** PP TIGR00112 69 PqdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevs 137 P+d+ e+la++++ + ++lliS++AG++++ le++l++ ++++R+mPNt+++v +++t++++++ v+ lcl|NCBI__GCF_000021925.1:WP_015944064.1 69 PKDVGEALAQIRE-GISSNQLLISVAAGIPLALLEKHLPH-CPIIRAMPNTSSAVLHSMTGLVKGQGVN 135 *********9998.88899*******************96.**************************** PP TIGR00112 138 eeqkelveellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206 e++++ ve+++ avGk+++++e++++ + a+sGSgPA+++l+ eal++agv +G+++e a++la++tl+ lcl|NCBI__GCF_000021925.1:WP_015944064.1 136 EAKQRDVEDIFGAVGKYIWITEEQINPLIAMSGSGPAYFYLFTEALVKAGVDMGFSQEVAENLAKETLM 204 ********************************************************************* PP TIGR00112 207 GaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrsee 262 Gaak+l++sg++p +L+ +VtsP+GtT+++l+v++e+g+++ v++a +a+++r++ lcl|NCBI__GCF_000021925.1:WP_015944064.1 205 GAAKMLAQSGKSPGELRVAVTSPKGTTQEALEVFREQGLEELVAQAAKACKHRAQA 260 *****************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (267 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: 8.94 // [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