Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate AZOBR_RS06245 AZOBR_RS06245 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__azobra:AZOBR_RS06245 Length = 275 Score = 177 bits (448), Expect = 3e-49 Identities = 109/264 (41%), Positives = 155/264 (58%), Gaps = 7/264 (2%) Query: 10 GAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAVADA---DV 66 G G M +++ G G+ A+ + +P + + G A+ V+ S +A+ DV Sbjct: 15 GCGKMGGAMLDGWLKAGI-ASSVAVIEPSGLPES-LRGNPAV-VLASGVDALPAGFAPDV 71 Query: 67 VVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMPNTPALL 126 VVL+VKPQ M +V A ++P + +S+AAG AS EA LG+ +VR MPNTPA + Sbjct: 72 VVLAVKPQVMDSVLPAYRALVRPGTVFLSVAAGKTIASFEAALGEGAAIVRSMPNTPAAI 131 Query: 127 RQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYFFLLMQA 186 +G + N V+ AQ LL AVG W++DE+ +D VTAVSGSGPAY FL+++A Sbjct: 132 GRGMTVAVGNPVVTEAQKSLCDSLLRAVGDVAWVEDESLLDPVTAVSGSGPAYVFLMVEA 191 Query: 187 MTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAAIKSFQA 246 M AGE GL E A RL T GA ++ S A+LR+ VTSPNGTT+AA+ A Sbjct: 192 MAKAGEAAGLPAELAMRLARATVAGAGELLHQSPTAAADLRKAVTSPNGTTQAALDVLMA 251 Query: 247 -NGFEALVEQALNAASQRSAELAE 269 +G + L ++A+ AA+ RS ELA+ Sbjct: 252 GDGMQPLFDRAVAAAANRSRELAK 275 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: 205 Number of extensions: 8 Number of successful extensions: 1 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 AZOBR_RS06245 AZOBR_RS06245 (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.2444.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-76 244.0 3.6 1.2e-76 243.8 3.6 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS06245 AZOBR_RS06245 pyrroline-5-carbox Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS06245 AZOBR_RS06245 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 243.8 3.6 1.2e-76 1.2e-76 3 263 .] 13 273 .. 11 273 .. 0.93 Alignments for each domain: == domain 1 score: 243.8 bits; conditional E-value: 1.2e-76 TIGR00112 3 iiGaGnmgeallsgllkkgakakkeilviers.eeklaalakelgvevtsdaeeavkeadvvllavKPq 70 + G+G+mg a+l g+lk+g + +++ vie+s +++ + ++ + da a + dvv+lavKPq lcl|FitnessBrowser__azobra:AZOBR_RS06245 13 LAGCGKMGGAMLDGWLKAGIA--SSVAVIEPSgLPESLRGNPAVVLASGVDALPAGFAPDVVVLAVKPQ 79 67***************9775..799999999755555555555556666667899999********** PP TIGR00112 71 dleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevsee 139 ++++vl ++ + +++++S++AG ti+ +e +l++ +++vR mPNt+a++g+g+t+++ + v+e+ lcl|FitnessBrowser__azobra:AZOBR_RS06245 80 VMDSVLPAYRA-LVRPGTVFLSVAAGKTIASFEAALGEGAAIVRSMPNTPAAIGRGMTVAVGNPVVTEA 147 *******9998.7789***************************************************** PP TIGR00112 140 qkelveellkavGkvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkG 207 qk+l ++ll+avG+v +ve e+lld vta+sGSgPA+vfl++ea+a+ag ++GLp+e+a++la++t++G lcl|FitnessBrowser__azobra:AZOBR_RS06245 148 QKSLCDSLLRAVGDVAWVEdESLLDPVTAVSGSGPAYVFLMVEAMAKAGEAAGLPAELAMRLARATVAG 216 ********************************************************************* PP TIGR00112 208 aaklleesgehpalLkdkVtsPgGtTiaglavLeekg.vrsavieaveaavkrseeL 263 a++ll++s +a L+++VtsP+GtT+a+l vL++++ ++ +++av aa++rs+eL lcl|FitnessBrowser__azobra:AZOBR_RS06245 217 AGELLHQSPTAAADLRKAVTSPNGTTQAALDVLMAGDgMQPLFDRAVAAAANRSREL 273 *********************************99866*****************98 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.35 // [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