Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; EC 1.5.1.2; PCA reductase (uncharacterized)
to candidate CA265_RS18505 CA265_RS18505 pyrroline-5-carboxylate reductase
Query= curated2:P74572 (267 letters) >FitnessBrowser__Pedo557:CA265_RS18505 Length = 269 Score = 133 bits (334), Expect = 5e-36 Identities = 90/268 (33%), Positives = 146/268 (54%), Gaps = 7/268 (2%) Query: 4 QLGIIGGGVMAEAILARLIAEKTYAPEEIIVGEPHGARR-DYLQKTYQVRVSPDNQEAAN 62 ++ IIG G + ++ L+ + II+ + A + Q+ Y +V+ +N +AA Sbjct: 3 KIAIIGSGNIGLSLAKGLVKANYTTTKNIILTRRNTANLYKFAQERY--KVTANNADAAA 60 Query: 63 VSEVLLLAVKPQVLDRVLASLAGGAN--RPLVISILAGVSLQRIQKGFPDHA-IIRAMPN 119 ++V++LAV PQ L+ VL + N + LVIS+++GVS +++ + IIRAMPN Sbjct: 61 DADVIILAVLPQQLNVVLEEIQSAINPAKHLVISVISGVSCAAVREKLDSNVQIIRAMPN 120 Query: 120 TPATVGAGMTAIAANKMVEPDQLAKAKAIFSAVGNVVEVPENLMDAVTGVSGSGPAYVAL 179 T +G MT IA++ P L +F VG+VV++ E+LM + T + G A+ Sbjct: 121 TAIAIGQSMTCIASDN-ASPQNLEDVTRMFETVGSVVKINEDLMTSATALCACGIAFFLR 179 Query: 180 MIEALADGGVLAGLPRAIAQKLALQTVLGTAELIKETEEHPAQIKDKVTSPGGTTIAGVA 239 I A + GGV G A K+A+QT G A+L+ HP DKVTSP G TIAG+ Sbjct: 180 GIRAASQGGVEIGFHADEALKMAVQTAKGAADLLLLHGTHPESEIDKVTSPKGCTIAGLN 239 Query: 240 VLEKMGFRSAIIEAVRAAYRRSQELGKK 267 +E G+ S++I+ ++ + ++ L K Sbjct: 240 EMEHNGYSSSLIKGIKLSALKAGNLYTK 267 Lambda K H 0.316 0.133 0.358 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: 149 Number of extensions: 8 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: 267 Length of database: 269 Length adjustment: 25 Effective length of query: 242 Effective length of database: 244 Effective search space: 59048 Effective search space used: 59048 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 CA265_RS18505 CA265_RS18505 (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.9406.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-70 222.6 6.6 3.9e-70 222.5 6.6 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS18505 CA265_RS18505 pyrroline-5-carbox Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS18505 CA265_RS18505 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 222.5 6.6 3.9e-70 3.9e-70 1 261 [. 4 262 .. 4 264 .. 0.96 Alignments for each domain: == domain 1 score: 222.5 bits; conditional E-value: 3.9e-70 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavK 68 iaiiG Gn+g +l++gl+k++ + k+i++++r++++l ++a+e +vt++++ a+++adv++lav lcl|FitnessBrowser__Pedo557:CA265_RS18505 4 IAIIGSGNIGLSLAKGLVKANYTTTKNIILTRRNTANLYKFAQER-YKVTANNADAAADADVIILAVL 70 89******************9999999999999999999998887.677777788999********** PP TIGR00112 69 PqdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassev 136 Pq+l+ vl+e++s + +++l+iS++ Gv++++++++l+++ +++R+mPNta ++g+++t ia + ++ lcl|FitnessBrowser__Pedo557:CA265_RS18505 71 PQQLNVVLEEIQSAINPAKHLVISVISGVSCAAVREKLDSNVQIIRAMPNTAIAIGQSMTCIASD-NA 137 *************99999********************************************999.79 PP TIGR00112 137 seeqkelveellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqt 204 s+++ e v++++++vG+vv+++e+l+ +tal+++g Af++ i a+ ++gv+ G+ ++ea+++a qt lcl|FitnessBrowser__Pedo557:CA265_RS18505 138 SPQNLEDVTRMFETVGSVVKINEDLMTSATALCACGIAFFLRGIRAASQGGVEIGFHADEALKMAVQT 205 99****************************************************************** PP TIGR00112 205 lkGaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrse 261 kGaa ll g hp+ +dkVtsP+G+Tiagl+++e++g s +i++++ ++ ++ lcl|FitnessBrowser__Pedo557:CA265_RS18505 206 AKGAADLLLLHGTHPESEIDKVTSPKGCTIAGLNEMEHNGYSSSLIKGIKLSALKAG 262 *************************************************99988775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (269 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: 00:00:00.01 # Mc/sec: 6.60 // [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