Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate N515DRAFT_1783 N515DRAFT_1783 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__Dyella79:N515DRAFT_1783 Length = 274 Score = 256 bits (653), Expect = 5e-73 Identities = 137/268 (51%), Positives = 180/268 (67%), Gaps = 1/268 (0%) Query: 5 RIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADA 64 RIAFIG GNMA SLIGGL G+ A+ + ++P AE R ++ EF + AVA+A Sbjct: 3 RIAFIGGGNMARSLIGGLLKTGIAASSVSVAEPRAEARQELGREFGVACYAEARPAVAEA 62 Query: 65 DVVVLSVKPQAMKAVCQALAPALKPEQ-LIVSIAAGIPCASLEAWLGQPRPVVRCMPNTP 123 +VVVL+VKPQ + A+ L L+ + +++SIAAG+ LE WLG P+VRCMPNTP Sbjct: 63 EVVVLAVKPQVLPALRNELQDVLRQRRPMLISIAAGVRIDQLERWLGGQLPIVRCMPNTP 122 Query: 124 ALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLL 183 AL+ GA+GL AN +VS Q A ++L A G+ W+DDEA +D VTA+SGSGPAYFF L Sbjct: 123 ALIGAGATGLCANGRVSPPQRALAQRILDAAGLTRWIDDEALMDTVTALSGSGPAYFFAL 182 Query: 184 MQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKS 243 ++A+ DA G+ RETA L QT LGA +M S PAELRRRVTSPNGTT+AA++S Sbjct: 183 VEALEDAAVAQGMPRETARALAAQTCLGAGRMLAESGEAPAELRRRVTSPNGTTQAALES 242 Query: 244 FQANGFEALVEQALNAASQRSAELAEQL 271 F A+G +V +A+ AA++R LA L Sbjct: 243 FAADGLPRIVARAVAAATRRGEALAAAL 270 Lambda K H 0.315 0.127 0.348 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: 218 Number of extensions: 5 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: 273 Length of database: 274 Length adjustment: 25 Effective length of query: 248 Effective length of database: 249 Effective search space: 61752 Effective search space used: 61752 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 N515DRAFT_1783 N515DRAFT_1783 (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.carbon/TIGR00112.hmm # target sequence database: /tmp/gapView.27552.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-89 285.3 0.8 2.9e-89 285.2 0.8 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_1783 N515DRAFT_1783 pyrroline-5-carbo Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_1783 N515DRAFT_1783 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 285.2 0.8 2.9e-89 2.9e-89 1 263 [] 4 266 .. 4 266 .. 0.98 Alignments for each domain: == domain 1 score: 285.2 bits; conditional E-value: 2.9e-89 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvlla 66 ia+iG+Gnm+++l+ gllk+g + ++++ v+e+++e++++l e+gv+ +++a+ av+ea+vv+la lcl|FitnessBrowser__Dyella79:N515DRAFT_1783 4 IAFIGGGNMARSLIGGLLKTGIA-ASSVSVAEPRAEARQELGREFGVACYAEARPAVAEAEVVVLA 68 89*****************9766.8***************************************** PP TIGR00112 67 vKPqdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaa 132 vKPq+l+++ +el++ +++ +liSi+AGv+i++le++l+++ ++vR+mPNt+a +gag+t+++a lcl|FitnessBrowser__Dyella79:N515DRAFT_1783 69 VKPQVLPALRNELQDVLRQRRPMLISIAAGVRIDQLERWLGGQLPIVRCMPNTPALIGAGATGLCA 134 ***************9999*********************************************** PP TIGR00112 133 ssevseeqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreea 197 + +vs+ q++l++++l+a G + +++ e+l+d+vtalsGSgPA++f l+eal+da+v++G+pre+a lcl|FitnessBrowser__Dyella79:N515DRAFT_1783 135 NGRVSPPQRALAQRILDAAGLTRWIDdEALMDTVTALSGSGPAYFFALVEALEDAAVAQGMPRETA 200 ****************************************************************** PP TIGR00112 198 kelaaqtlkGaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 ++laaqt Ga+++l+esge pa+L+ +VtsP+GtT+a+l+++ ++g+ + v++av aa++r e L lcl|FitnessBrowser__Dyella79:N515DRAFT_1783 201 RALAAQTCLGAGRMLAESGEAPAELRRRVTSPNGTTQAALESFAADGLPRIVARAVAAATRRGEAL 266 **************************************************************8865 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6.77 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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