Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate WP_086510436.1 BZY95_RS13455 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >NCBI__GCF_002151265.1:WP_086510436.1 Length = 274 Score = 271 bits (694), Expect = 9e-78 Identities = 141/270 (52%), Positives = 188/270 (69%), Gaps = 1/270 (0%) Query: 5 RIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADA 64 R+ FIGAGNMA+++IGG+ G PA I A+ P A + + I N AV DA Sbjct: 4 RVTFIGAGNMASAIIGGMIDNGHPATAITATSPSDAFLAPVHERYGIRTNTDNQAAVRDA 63 Query: 65 DVVVLSVKPQAMKAVCQALAPALKPEQ-LIVSIAAGIPCASLEAWLGQPRPVVRCMPNTP 123 D+VVL+VKPQ M+ VC+ L L+ ++ LI+S+AAG+ SL+AW+G P+VRCMPNTP Sbjct: 64 DIVVLAVKPQVMREVCEGLRDTLQRQRPLIISVAAGLTAESLQAWMGGGLPLVRCMPNTP 123 Query: 124 ALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLL 183 +L+ GA+GLYA A+VS Q QA +LL AVG+ W++ EA +DAVTAVSGSGPAYFFL+ Sbjct: 124 SLVGAGAAGLYATAEVSDEQRAQATELLEAVGLVEWVEQEALLDAVTAVSGSGPAYFFLM 183 Query: 184 MQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKS 243 +AM +AG KLGL ETA RL +QTALGAA+MA SE+ P L+R V SP GTTE A++ Sbjct: 184 FEAMEEAGVKLGLPAETARRLAIQTALGAARMAQQSELTPDRLKRNVMSPGGTTERAVEH 243 Query: 244 FQANGFEALVEQALNAASQRSAELAEQLGQ 273 + G +V A++A + R+ E+AE+LGQ Sbjct: 244 MEQAGLRGIVADAMDACAARAREMAEELGQ 273 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: 208 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: 274 Length adjustment: 25 Effective length of query: 248 Effective length of database: 249 Effective search space: 61752 Effective search space used: 61752 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_086510436.1 BZY95_RS13455 (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.14380.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-89 286.3 3.2 1.5e-89 286.1 3.2 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086510436.1 BZY95_RS13455 pyrroline-5-carbox Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086510436.1 BZY95_RS13455 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 286.1 3.2 1.5e-89 1.5e-89 1 263 [] 5 267 .. 5 267 .. 0.99 Alignments for each domain: == domain 1 score: 286.1 bits; conditional E-value: 1.5e-89 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 +++iGaGnm++a++ g++ +g + ++ i + +s++ la ++++g+++++d+++av++ad+v+lavKP lcl|NCBI__GCF_002151265.1:WP_086510436.1 5 VTFIGAGNMASAIIGGMIDNGHP-ATAITATSPSDAFLAPVHERYGIRTNTDNQAAVRDADIVVLAVKP 72 68******************988.7999999999*********************************** PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 q+++ev++ l+++ +++ l+iS++AG+t+e l+ ++++ ++vR+mPNt++ vgag+++++a++evs+ lcl|NCBI__GCF_002151265.1:WP_086510436.1 73 QVMREVCEGLRDTLQRQRPLIISVAAGLTAESLQAWMGGGLPLVRCMPNTPSLVGAGAAGLYATAEVSD 141 ************9999***************************************************** PP TIGR00112 139 eqkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206 eq+++++ell+avG v +ve e+lldavta+sGSgPA++fl++ea+++agvklGLp+e+a++la qt lcl|NCBI__GCF_002151265.1:WP_086510436.1 142 EQRAQATELLEAVGLVEWVEqEALLDAVTAVSGSGPAYFFLMFEAMEEAGVKLGLPAETARRLAIQTAL 210 ********************************************************************* PP TIGR00112 207 GaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 Gaa++ ++s+ +p +Lk +V+sPgGtT ++++ +e++g+r+ v++a++a+++r++e+ lcl|NCBI__GCF_002151265.1:WP_086510436.1 211 GAARMAQQSELTPDRLKRNVMSPGGTTERAVEHMEQAGLRGIVADAMDACAARAREM 267 *********99*******************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (274 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: 8.35 // [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