Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate SMc02677 SMc02677 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__Smeli:SMc02677 Length = 272 Score = 184 bits (467), Expect = 2e-51 Identities = 110/265 (41%), Positives = 153/265 (57%), Gaps = 4/265 (1%) Query: 6 IAFIGAGNMAASLIGGLRAQGVPAAQIRASDPG-AEQRAKIAGEFAIDVVESNAEAVADA 64 I +GAGNM +++ G GV + + DPG + AK+ + + S A A A Sbjct: 9 IVLVGAGNMGGAMLAGWLKSGVRGSDVLVIDPGPSPAMAKLLADSGVQHATS-APAGGKA 67 Query: 65 DVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPA 124 + L+VKPQ M+ V L + P+ +IVS+AAG +E LG+ VR MPNTPA Sbjct: 68 GAIFLAVKPQVMETVLPPLKGLVGPQTVIVSVAAGKTLGFIERHLGEAA-TVRAMPNTPA 126 Query: 125 LLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLM 184 ++ +G +G +ANA+VS AQ LL G W+ EA IDAVTAVSGSGPAY F L+ Sbjct: 127 MIGRGVTGAFANARVSEAQRALVHDLLKVSGPVEWVGSEADIDAVTAVSGSGPAYVFYLV 186 Query: 185 QAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKSF 244 + M +AG K GL + A RL +T GA ++ S + A LR+ VTSP GTT AA+ Sbjct: 187 ECMAEAGRKAGLEADLAMRLARETVAGAGELLHQSPDDAARLRQNVTSPGGTTAAALAVL 246 Query: 245 QA-NGFEALVEQALNAASQRSAELA 268 A +G + L ++A+ AA +R+ ELA Sbjct: 247 MADDGMQPLFDRAIAAARKRAEELA 271 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: 6 Number of successful extensions: 3 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 SMc02677 SMc02677 (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.7117.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-85 271.1 2.6 6.2e-85 271.0 2.6 1.0 1 lcl|FitnessBrowser__Smeli:SMc02677 SMc02677 pyrroline-5-carboxylate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc02677 SMc02677 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 271.0 2.6 6.2e-85 6.2e-85 1 263 [] 9 270 .. 9 270 .. 0.96 Alignments for each domain: == domain 1 score: 271.0 bits; conditional E-value: 6.2e-85 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilviers.eeklaalakelgvevtsdaeeavkeadvvllavKPqdlee 74 i+++GaGnmg a+l+g+lk+g++ +++lvi++ ++++a+l+++ gv+ +++ + a +a ++lavKPq++e+ lcl|FitnessBrowser__Smeli:SMc02677 9 IVLVGAGNMGGAMLAGWLKSGVR-GSDVLVIDPGpSPAMAKLLADSGVQHATS-APAGGKAGAIFLAVKPQVMET 81 789*****************998.8*********7777888888888888777.589999*************** PP TIGR00112 75 vlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellk 149 vl lk+ +++++S++AG t+ +e++l+ e+++vR+mPNt+a++g+gvt+++a+++vse+q++lv++llk lcl|FitnessBrowser__Smeli:SMc02677 82 VLPPLKG-LVGPQTVIVSVAAGKTLGFIERHLG-EAATVRAMPNTPAMIGRGVTGAFANARVSEAQRALVHDLLK 154 *******.7779********************7.599************************************** PP TIGR00112 150 avGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalLk 223 G v +v e+++davta+sGSgPA+vf+l+e++a+ag k+GL++++a++la++t++Ga++ll++s +++a+L+ lcl|FitnessBrowser__Smeli:SMc02677 155 VSGPVEWVGsEADIDAVTAVSGSGPAYVFYLVECMAEAGRKAGLEADLAMRLARETVAGAGELLHQSPDDAARLR 229 *************************************************************************** PP TIGR00112 224 dkVtsPgGtTiaglavLeekg.vrsavieaveaavkrseeL 263 ++VtsPgGtT+a+lavL++++ ++ +++a+ aa kr+eeL lcl|FitnessBrowser__Smeli:SMc02677 230 QNVTSPGGTTAAALAVLMADDgMQPLFDRAIAAARKRAEEL 270 ****************998765*****************98 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.73 // [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