Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_046007574.1 OLEAN_RS00385 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_000967895.1:WP_046007574.1 Length = 281 Score = 283 bits (724), Expect = 3e-81 Identities = 152/276 (55%), Positives = 193/276 (69%), Gaps = 3/276 (1%) Query: 1 MSTPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEA 60 MS + FIG GNMA SLIGGL AQG I SDP QR ++ ++ ++ A Sbjct: 1 MSMSNVCFIGGGNMATSLIGGLIAQGHAPESISVSDPNESQREQLIKQYGVNAFADCGPA 60 Query: 61 VADADVVVLSVKPQAMKAVCQALAPALK---PEQLIVSIAAGIPCASLEAWLGQPRPVVR 117 + +AD+VVL+VKPQ MK V + ALK + L VSIAAGI SL++WLG+ + +VR Sbjct: 61 MENADIVVLAVKPQVMKDVALMITTALKGFAKQPLFVSIAAGINLFSLQSWLGEKQAIVR 120 Query: 118 CMPNTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGP 177 CMPNTP+L++ GASGL+AN Q S Q A +L A GI W+ EA+IDAVTAVSGSGP Sbjct: 121 CMPNTPSLIQLGASGLFANEQTSIVQKNLAETVLKAAGIVQWVQSEAEIDAVTAVSGSGP 180 Query: 178 AYFFLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTT 237 AY+FL M+AM DAG +LGLSRETAS LT+QTA+GAA MA S+V+ AELRRRVTSP GTT Sbjct: 181 AYYFLFMEAMIDAGVELGLSRETASELTMQTAIGAAHMAKQSDVDVAELRRRVTSPGGTT 240 Query: 238 EAAIKSFQANGFEALVEQALNAASQRSAELAEQLGQ 273 E AI +F++ +V+ AL AA++RS ELA+ LG+ Sbjct: 241 EQAINTFESAHLRDIVKAALAAANRRSGELAQLLGE 276 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: 202 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: 281 Length adjustment: 25 Effective length of query: 248 Effective length of database: 256 Effective search space: 63488 Effective search space used: 63488 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_046007574.1 OLEAN_RS00385 (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.16687.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-82 261.6 5.0 5.1e-82 261.4 5.0 1.0 1 lcl|NCBI__GCF_000967895.1:WP_046007574.1 OLEAN_RS00385 pyrroline-5-carbox Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000967895.1:WP_046007574.1 OLEAN_RS00385 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 261.4 5.0 5.1e-82 5.1e-82 1 263 [] 6 270 .. 6 270 .. 0.98 Alignments for each domain: == domain 1 score: 261.4 bits; conditional E-value: 5.1e-82 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 + +iG+Gnm+++l+ gl+++g + +++i v +++e+++++l+k++gv++ +d a+++ad+v+lavKP lcl|NCBI__GCF_000967895.1:WP_046007574.1 6 VCFIGGGNMATSLIGGLIAQGHA-PESISVSDPNESQREQLIKQYGVNAFADCGPAMENADIVVLAVKP 73 579****************9876.9******************************************** PP TIGR00112 70 qdleevlaelks..eektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassev 136 q++++v+ ++++ + +k+ l++Si+AG+++ l+++l++++++vR+mPNt++ ++ g+++++a++++ lcl|NCBI__GCF_000967895.1:WP_046007574.1 74 QVMKDVALMITTalKGFAKQPLFVSIAAGINLFSLQSWLGEKQAIVRCMPNTPSLIQLGASGLFANEQT 142 *******999997777889***********************************************999 PP TIGR00112 137 seeqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqt 204 s qk+l+e +lka G v +v+ e+++davta+sGSgPA+ fl++ea++dagv+lGL+re+a el++qt lcl|NCBI__GCF_000967895.1:WP_046007574.1 143 SIVQKNLAETVLKAAGIVQWVQsEAEIDAVTAVSGSGPAYYFLFMEAMIDAGVELGLSRETASELTMQT 211 999****************************************************************** PP TIGR00112 205 lkGaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 +Gaa++ ++s+ + a+L+ +VtsPgGtT ++++++e +++r+ v +a+ aa +rs eL lcl|NCBI__GCF_000967895.1:WP_046007574.1 212 AIGAAHMAKQSDVDVAELRRRVTSPGGTTEQAINTFESAHLRDIVKAALAAANRRSGEL 270 *******************************************************9887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (281 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: 00:00:00.00 # Mc/sec: 10.55 // [ok]
This GapMind analysis is from Sep 24 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