Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_029910292.1 P166_RS0106935 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_000711315.1:WP_029910292.1 Length = 285 Score = 264 bits (675), Expect = 1e-75 Identities = 139/271 (51%), Positives = 187/271 (69%), Gaps = 1/271 (0%) Query: 2 STPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAV 61 S +I+FIG+GNMA SLI GL A G PA I A+DP +R I+ I +E NA AV Sbjct: 3 SNIKISFIGSGNMALSLIKGLIASGFPATNIIATDPNESKRQSISQTLGIACLEDNASAV 62 Query: 62 ADADVVVLSVKPQAMKAVCQALAPALKPEQ-LIVSIAAGIPCASLEAWLGQPRPVVRCMP 120 A +D+VVL++KPQ ++ VC + A++ + LI+S+AAG+ + WLG VVRCMP Sbjct: 63 AQSDIVVLAIKPQVLQNVCTEVGGAMQQKNPLIISVAAGVRATDIVRWLGGKVAVVRCMP 122 Query: 121 NTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYF 180 NTPA+++ GA+GLYAN VS Q QA +L AVGI +W+ E+ +D VTAVSGSGPAY+ Sbjct: 123 NTPAMIQSGATGLYANEFVSEEQKSQAENILRAVGITVWVKTESDLDTVTAVSGSGPAYY 182 Query: 181 FLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAA 240 FL M+AM A + +GLS + A LT+QTA GAA+MAL S + A+LRR VTSPNGTTE A Sbjct: 183 FLFMEAMQKAAQGMGLSEQAARILTIQTAFGAAKMALESSEDCAQLRRNVTSPNGTTEKA 242 Query: 241 IKSFQANGFEALVEQALNAASQRSAELAEQL 271 I+SF++N E +V +A+ A R+ LA++L Sbjct: 243 IQSFESNRLEDIVAEAMMCAKLRAETLADEL 273 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: 187 Number of extensions: 7 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: 285 Length adjustment: 26 Effective length of query: 247 Effective length of database: 259 Effective search space: 63973 Effective search space used: 63973 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 WP_029910292.1 P166_RS0106935 (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.31504.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-82 262.2 7.4 3.4e-82 262.0 7.4 1.0 1 lcl|NCBI__GCF_000711315.1:WP_029910292.1 P166_RS0106935 pyrroline-5-carbo Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711315.1:WP_029910292.1 P166_RS0106935 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 262.0 7.4 3.4e-82 3.4e-82 1 263 [] 7 269 .. 7 269 .. 0.99 Alignments for each domain: == domain 1 score: 262.0 bits; conditional E-value: 3.4e-82 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 i++iG Gnm+ +l++gl+++g + +++i+ ++++e+k++ ++lg++ +d+++av+++d+v+la+KP lcl|NCBI__GCF_000711315.1:WP_029910292.1 7 ISFIGSGNMALSLIKGLIASGFP-ATNIIATDPNESKRQSISQTLGIACLEDNASAVAQSDIVVLAIKP 74 79******************998.89******************************************* PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 q+l++v++e+ + ++k+ l+iS++AGv++ ++ ++l+++ +vvR+mPNt+a++++g+t+++a+++vse lcl|NCBI__GCF_000711315.1:WP_029910292.1 75 QVLQNVCTEVGGAMQQKNPLIISVAAGVRATDIVRWLGGKVAVVRCMPNTPAMIQSGATGLYANEFVSE 143 ************9999***************************************************** PP TIGR00112 139 eqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206 eqk+++e++l+avG +v+v+ e++ld+vta+sGSgPA+ fl++ea+++a+ +GL+++ a+ l+ qt lcl|NCBI__GCF_000711315.1:WP_029910292.1 144 EQKSQAENILRAVGITVWVKtESDLDTVTAVSGSGPAYYFLFMEAMQKAAQGMGLSEQAARILTIQTAF 212 ********************************************************************* PP TIGR00112 207 GaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 Gaak+ es+e+ a+L+ +VtsP+GtT ++++++e +++++ v+ea+ a+ r+e L lcl|NCBI__GCF_000711315.1:WP_029910292.1 213 GAAKMALESSEDCAQLRRNVTSPNGTTEKAIQSFESNRLEDIVAEAMMCAKLRAETL 269 **************************************************9999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (285 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: 7.13 // [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