Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate WP_053936293.1 WG78_RS02925 pyrroline-5-carboxylate reductase
Query= BRENDA::O87725 (266 letters) >NCBI__GCF_001294205.1:WP_053936293.1 Length = 263 Score = 210 bits (535), Expect = 2e-59 Identities = 117/262 (44%), Positives = 162/262 (61%), Gaps = 2/262 (0%) Query: 5 IGFIGCGNMAQAMISALVKSKLIESNQIIVSNRSKNILEKMNKEYGITIAANNIEVAEKC 64 IGFIG GNMA AMI+ L S QI NRS L + YG+ IA + ++A + Sbjct: 3 IGFIGTGNMASAMIAGLHSSH--PDWQIHGFNRSMGKLTDLQTRYGLQIAQSLEDLAARA 60 Query: 65 DIVFLAVKQNLYEMVMKEIKDSVTKDKIFVSIAPGKTMEFLEAHLGAYAKILRTMPNTPS 124 D++ LAVK Y+ ++ + + V++A G T+ +++H+G I+R+MPNTP+ Sbjct: 61 DVLVLAVKPQGYDAMLATLAPPLQARHTLVTVAVGYTIARVQSHIGTQTHIVRSMPNTPA 120 Query: 125 MVSEGMTAICPNSNIASEELELLVKLIESFGAVEIIEEKLFDAVVAVSGSSPAYVFMFIE 184 V GM+A+C ++ + + + ESFG I E FD A++GSSPA+V+M IE Sbjct: 121 SVGAGMSALCGSAGLPEARRSDVTAVFESFGRAVWIAEGQFDVFSAIAGSSPAWVYMMIE 180 Query: 185 AMADAAVIQGMPRAQAYRFAAQAVLGSAKMVLESKSHPGELKDMVCSPGGTTIEAVAVLE 244 AMADAAV GMPRAQAY +QAVLGSA++V +S HPG LKD VCSPGGTTI VA LE Sbjct: 181 AMADAAVQNGMPRAQAYAVISQAVLGSAQLVRDSGQHPGVLKDQVCSPGGTTIAGVAALE 240 Query: 245 ERGMRSAVIEAMRKCAQKSKEM 266 + GMR+A EA+ ++K + Sbjct: 241 KAGMRNAWFEAVNATLARTKAL 262 Lambda K H 0.317 0.130 0.349 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: 161 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: 266 Length of database: 263 Length adjustment: 25 Effective length of query: 241 Effective length of database: 238 Effective search space: 57358 Effective search space used: 57358 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_053936293.1 WG78_RS02925 (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.1811756.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-83 264.0 1.8 9.6e-83 263.8 1.8 1.0 1 NCBI__GCF_001294205.1:WP_053936293.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001294205.1:WP_053936293.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 263.8 1.8 9.6e-83 9.6e-83 1 263 [] 3 262 .. 3 262 .. 0.97 Alignments for each domain: == domain 1 score: 263.8 bits; conditional E-value: 9.6e-83 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdle 73 i++iG Gnm++a+++gl+++ + +i+ +rs kl++l +++g + +++ e +++ adv++lavKPq + NCBI__GCF_001294205.1:WP_053936293.1 3 IGFIGTGNMASAMIAGLHSS--HPDWQIHGFNRSMGKLTDLQTRYGLQIAQSLEDLAARADVLVLAVKPQGYD 73 89**************9998..4479*********************************************** PP TIGR00112 74 evlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelvee 146 ++la+l+ ++ ++l++++ G ti+++++++++++++vR mPNt+a+vgag++a++ s+ e++++ v++ NCBI__GCF_001294205.1:WP_053936293.1 74 AMLATLAP-PLQARHTLVTVAVGYTIARVQSHIGTQTHIVRSMPNTPASVGAGMSALCGSAGLPEARRSDVTA 145 *******9.4457899***********************************************999******* PP TIGR00112 147 llkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehp 219 +++++G +v+++e ++d + a++GS+PA+v+++iea+ada+v++G+pr++a+++++q++ G+a+l+ sg+hp NCBI__GCF_001294205.1:WP_053936293.1 146 VFESFGRAVWIAEGQFDVFSAIAGSSPAWVYMMIEAMADAAVQNGMPRAQAYAVISQAVLGSAQLVRDSGQHP 218 ************************************************************************* PP TIGR00112 220 alLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 +Lkd+V+sPgGtTiag+a+Le++g+r+a eav+a+ +r++ L NCBI__GCF_001294205.1:WP_053936293.1 219 GVLKDQVCSPGGTTIAGVAALEKAGMRNAWFEAVNATLARTKAL 262 ****************************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (263 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: 9.97 // [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