Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate 7023985 Shewana3_1193 pyrroline-5-carboxylate reductase (RefSeq)
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__ANA3:7023985 Length = 272 Score = 210 bits (534), Expect = 3e-59 Identities = 117/269 (43%), Positives = 167/269 (62%), Gaps = 1/269 (0%) Query: 1 MSTPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEA 60 MS +I FIGAGNM S+I GL G PAA ++A++P + +A +F + V + N A Sbjct: 1 MSQQKICFIGAGNMTRSIISGLIRSGYPAALVQATNPSQGKLDALAADFGVRVSQDNFSA 60 Query: 61 VADADVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMP 120 DADV+VLSVKPQ M+ VCQAL +L+++IAAGI +L Q +VR MP Sbjct: 61 AQDADVIVLSVKPQLMEQVCQALQGIDMSNKLVITIAAGIKAERYSQYLAQSITLVRTMP 120 Query: 121 NTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYF 180 NTP + G +GLYA +S AQ A +L+S+ G +W+++E++I+ V A++GS PAYF Sbjct: 121 NTPMQIGVGMTGLYAPQPLSDAQQAIAERLMSSGGEIVWVNEESEINQVIALAGSSPAYF 180 Query: 181 FLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSS-EVEPAELRRRVTSPNGTTEA 239 FLLM++M DAG+++G+ A L Q ALGAA MA + E+ LR VTS GTT Sbjct: 181 FLLMESMIDAGKQMGMDEAKARSLVQQAALGAAMMAKQNPELTLGNLRENVTSKGGTTAQ 240 Query: 240 AIKSFQANGFEALVEQALNAASQRSAELA 268 AI +F+A +V+ A+ +R+ E+A Sbjct: 241 AIATFEAADLRGVVKNAMENCIKRAEEMA 269 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: 160 Number of extensions: 8 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: 272 Length adjustment: 25 Effective length of query: 248 Effective length of database: 247 Effective search space: 61256 Effective search space used: 61256 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 7023985 Shewana3_1193 (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.carbon/TIGR00112.hmm # target sequence database: /tmp/gapView.21888.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-77 247.0 7.5 1.4e-77 246.9 7.5 1.0 1 lcl|FitnessBrowser__ANA3:7023985 Shewana3_1193 pyrroline-5-carbox Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7023985 Shewana3_1193 pyrroline-5-carboxylate reductase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 246.9 7.5 1.4e-77 1.4e-77 1 263 [] 6 268 .. 6 268 .. 0.98 Alignments for each domain: == domain 1 score: 246.9 bits; conditional E-value: 1.4e-77 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevla 77 i +iGaGnm ++++sgl+++g + ++ + +++s+ kl+ala+++gv+v++d+ +a+++adv++l+vKPq +e+v++ lcl|FitnessBrowser__ANA3:7023985 6 ICFIGAGNMTRSIISGLIRSGYP-AALVQATNPSQGKLDALAADFGVRVSQDNFSAAQDADVIVLSVKPQLMEQVCQ 81 68******************887.7899999999******************************************* PP TIGR00112 78 elkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellkavGkv 154 l++ ++ +kl+i+i+AG+++e+++q+l+++ ++vR mPNt+ ++g g+t+++a ++ s++q++ +e+l+++ G++ lcl|FitnessBrowser__ANA3:7023985 82 ALQG-IDMSNKLVITIAAGIKAERYSQYLAQSITLVRTMPNTPMQIGVGMTGLYAPQPLSDAQQAIAERLMSSGGEI 157 ****.66699******************************************************************* PP TIGR00112 155 veve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesge.hpalLkdkVtsP 229 v+v+ e+++++v al+GS+PA++fll+e+++dag ++G+++++a++l++q+ Gaa + +++ e + L+++Vts+ lcl|FitnessBrowser__ANA3:7023985 158 VWVNeESEINQVIALAGSSPAYFFLLMESMIDAGKQMGMDEAKARSLVQQAALGAAMMAKQNPElTLGNLRENVTSK 234 ****999******************************************************99999*********** PP TIGR00112 230 gGtTiaglavLeekgvrsavieaveaavkrseeL 263 gGtT++++a++e++++r+ v +a+e+++kr+ee+ lcl|FitnessBrowser__ANA3:7023985 235 GGTTAQAIATFEAADLRGVVKNAMENCIKRAEEM 268 *******************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (272 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.89 // [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