Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_012758436.1 RLEG_RS14900 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_000023185.1:WP_012758436.1 Length = 275 Score = 184 bits (467), Expect = 2e-51 Identities = 112/272 (41%), Positives = 157/272 (57%), Gaps = 10/272 (3%) Query: 2 STPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAE----QRAKIAGEFAIDVVESN 57 ST + IGAGNM +++ G GVP + + DPG AG + + ++ Sbjct: 8 STHPVVLIGAGNMGGAMLSGWLKSGVPGSAVIVVDPGPSPAMLSTISEAGATHLTALPTD 67 Query: 58 AEAVADADVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVR 117 +A V+ L+VKPQ M+ V A+ A+ PE ++VS+AAG LE LG+ +VR Sbjct: 68 LKA----SVLFLAVKPQVMETVLPAVKSAVGPETVVVSVAAGKTLGFLERHLGKAA-MVR 122 Query: 118 CMPNTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGP 177 MPNTPA++ +G +G +ANA V+ Q E+ LL G W+ EA IDAVTA+SGSGP Sbjct: 123 AMPNTPAMVGRGVTGAFANAGVNDQQRERVHSLLRVSGPVEWVPAEADIDAVTALSGSGP 182 Query: 178 AYFFLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTT 237 AY F L++ M +AG KLGL + A RL +T GA ++ S + + LR VTSP GTT Sbjct: 183 AYVFYLVECMAEAGRKLGLQADLAMRLARETVAGAGELMHQSPDDASRLRENVTSPGGTT 242 Query: 238 EAAIKSFQA-NGFEALVEQALNAASQRSAELA 268 AA+ A +G + L + AL AA +R+ ELA Sbjct: 243 AAALAVLMAEDGMQPLFDAALAAARKRAEELA 274 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: 194 Number of extensions: 10 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: 275 Length adjustment: 25 Effective length of query: 248 Effective length of database: 250 Effective search space: 62000 Effective search space used: 62000 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_012758436.1 RLEG_RS14900 (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.6145.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-82 260.7 3.2 9.2e-82 260.6 3.2 1.0 1 lcl|NCBI__GCF_000023185.1:WP_012758436.1 RLEG_RS14900 pyrroline-5-carboxy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023185.1:WP_012758436.1 RLEG_RS14900 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.6 3.2 9.2e-82 9.2e-82 1 263 [] 12 273 .. 12 273 .. 0.95 Alignments for each domain: == domain 1 score: 260.6 bits; conditional E-value: 9.2e-82 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilviers.eeklaalakelgvevtsdaeeavkeadvvllavK 68 +++iGaGnmg a+lsg+lk+g++ + ++v+++ ++++ + e+g++ ++ +a+v++lavK lcl|NCBI__GCF_000023185.1:WP_012758436.1 12 VVLIGAGNMGGAMLSGWLKSGVP-GSAVIVVDPGpSPAMLSTISEAGATHLTALP-TDLKASVLFLAVK 78 579*****************998.7999999999788888999999988888865.566778******* PP TIGR00112 69 PqdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevs 137 Pq++e+vl +ks e++++S++AG t+ le++l+ ++++vR+mPNt+a+vg+gvt+++a++ v+ lcl|NCBI__GCF_000023185.1:WP_012758436.1 79 PQVMETVLPAVKS-AVGPETVVVSVAAGKTLGFLERHLG-KAAMVRAMPNTPAMVGRGVTGAFANAGVN 145 *********9999.8889********************8.599************************** PP TIGR00112 138 eeqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtl 205 ++q+e+v++ll+ G v +v+ e+++davtalsGSgPA+vf+l+e++a+ag klGL++++a++la++t+ lcl|NCBI__GCF_000023185.1:WP_012758436.1 146 DQQRERVHSLLRVSGPVEWVPaEADIDAVTALSGSGPAYVFYLVECMAEAGRKLGLQADLAMRLARETV 214 ********************************************************************* PP TIGR00112 206 kGaaklleesgehpalLkdkVtsPgGtTiaglavLeekg.vrsavieaveaavkrseeL 263 +Ga++l+++s +++++L+++VtsPgGtT+a+lavL++++ ++ +++a+ aa kr+eeL lcl|NCBI__GCF_000023185.1:WP_012758436.1 215 AGAGELMHQSPDDASRLRENVTSPGGTTAAALAVLMAEDgMQPLFDAALAAARKRAEEL 273 **********************************987655****************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (275 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: 10.33 // [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