Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate GFF288 HP15_287 pyrroline-5-carboxylate reductase
Query= SwissProt::P22008 (273 letters) >FitnessBrowser__Marino:GFF288 Length = 277 Score = 234 bits (598), Expect = 1e-66 Identities = 123/271 (45%), Positives = 177/271 (65%), Gaps = 1/271 (0%) Query: 2 STPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEAV 61 ++P I+FIGAGNMA+++IGG+ G A I S P I F + V N Sbjct: 3 TSPTISFIGAGNMASAIIGGMLDNGYKAGNIWVSAPDDAHLQTIRKRFGVSVTTDNRYCA 62 Query: 62 ADADVVVLSVKPQAMKAVCQALAPALKPEQ-LIVSIAAGIPCASLEAWLGQPRPVVRCMP 120 AD+VVL+VKPQ M VC+ +AP ++ + L+VSIAAG+ +L+ WLG P+VR MP Sbjct: 63 QQADMVVLAVKPQVMADVCRDIAPVVQNTRPLMVSIAAGLTADTLDGWLGGGLPMVRVMP 122 Query: 121 NTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYF 180 NTP+L+ +GA+GL+AN +V Q + + ++G ALW++DE + AVTA+SGSGPAYF Sbjct: 123 NTPSLVGKGAAGLFANKEVKDKQKKMVESVFESIGSALWVEDENLLHAVTALSGSGPAYF 182 Query: 181 FLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSEVEPAELRRRVTSPNGTTEAA 240 FL+++A+ +A + G++ TA L +QT GAA+MA SE +P +L+R V SP GTTE A Sbjct: 183 FLMLEALEEAATEAGIAAGTARELAIQTMAGAAEMAGRSEHDPGQLKRNVMSPGGTTEQA 242 Query: 241 IKSFQANGFEALVEQALNAASQRSAELAEQL 271 I +F+ G LV +A AA +RS E+A++L Sbjct: 243 INTFEEGGMRDLVAKAYKAAFKRSEEMAKEL 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: 190 Number of extensions: 6 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: 277 Length adjustment: 25 Effective length of query: 248 Effective length of database: 252 Effective search space: 62496 Effective search space used: 62496 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 GFF288 HP15_287 (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.2871.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-88 283.2 1.4 1.3e-88 283.1 1.4 1.0 1 lcl|FitnessBrowser__Marino:GFF288 HP15_287 pyrroline-5-carboxylate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF288 HP15_287 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 283.1 1.4 1.3e-88 1.3e-88 1 263 [] 7 269 .. 7 269 .. 0.99 Alignments for each domain: == domain 1 score: 283.1 bits; conditional E-value: 1.3e-88 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevl 76 i++iGaGnm++a++ g+l +g k + +i+v ++ +++l+ k++gv+vt+d++ ++++ad+v+lavKPq++ +v+ lcl|FitnessBrowser__Marino:GFF288 7 ISFIGAGNMASAIIGGMLDNGYK-AGNIWVSAPDDAHLQTIRKRFGVSVTTDNRYCAQQADMVVLAVKPQVMADVC 81 79*****************9877.8*************************************************** PP TIGR00112 77 aelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellkavG 152 ++++ ++ l++Si+AG+t+++l +l++ ++vRvmPNt++ vg+g+++++a++ev+++qk+ ve++++++G lcl|FitnessBrowser__Marino:GFF288 82 RDIAPVVQNTRPLMVSIAAGLTADTLDGWLGGGLPMVRVMPNTPSLVGKGAAGLFANKEVKDKQKKMVESVFESIG 157 *****99999****************************************************************** PP TIGR00112 153 kvveve.eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalLkdkVt 227 ++++ve e+ll+avtalsGSgPA++fl++eal++a++++G+ + +a+ela qt++Gaa++ +s+++p +Lk +V+ lcl|FitnessBrowser__Marino:GFF288 158 SALWVEdENLLHAVTALSGSGPAYFFLMLEALEEAATEAGIAAGTARELAIQTMAGAAEMAGRSEHDPGQLKRNVM 233 ****************************************************************9*********** PP TIGR00112 228 sPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 sPgGtT ++++++ee+g+r+ v++a +aa krsee+ lcl|FitnessBrowser__Marino:GFF288 234 SPGGTTEQAINTFEEGGMRDLVAKAYKAAFKRSEEM 269 *********************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (277 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: 8.97 // [ok]
This GapMind analysis is from Apr 09 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