Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate WP_012506656.1 PAES_RS10560 pyrroline-5-carboxylate reductase
Query= BRENDA::G7KRM5 (274 letters) >NCBI__GCF_000020625.1:WP_012506656.1 Length = 266 Score = 173 bits (438), Expect = 4e-48 Identities = 101/263 (38%), Positives = 157/263 (59%), Gaps = 4/263 (1%) Query: 12 TLGFIGAGKMAESIAKGAVRSGVLSPSRIKTAIHSNPARRTAFESIGITVLSSNDDVVRD 71 ++GF+G G++A ++ G V +RI A + GI SS +V RD Sbjct: 5 SIGFVGTGRIARALISGLVNDPA---NRICGYDKDPDAIAAVVKQFGIEGTSSAAEVARD 61 Query: 72 SNVVVFSVKPQLLKDVVLKLKPLLTKDKLLVSVAAGIKMKDLQEWA-GHERFIRVMPNTA 130 + +++ +VKP + +VV +L+P LT LL+SVAAGI + +++ + R IRVMPNT Sbjct: 62 ARIIILAVKPYQIGEVVEELRPHLTTGHLLISVAAGITSEFIRQHSIDAMRVIRVMPNTP 121 Query: 131 ATVGEAASVMSLGGAATEEDANLISQLFGSIGKIWKADDKYFDAITGLSGSGPAYIYLAI 190 A G+ + +S G AT+ED L + +F +IG++ D++ DA T +SGSGPAY++ I Sbjct: 122 AFTGQGMTALSKGIMATQEDIALATTMFSAIGRVAVLDERLMDAATAVSGSGPAYMFSLI 181 Query: 191 EALADGGVAAGLPRDLALSLASQTVLGAASMATQSGKHPGQLKDDVTSPGGTTIAGVHEL 250 ++A+GG GL A+ L++QT+LGAA+M K P +L +VT+PGGTT AG+ ++ Sbjct: 182 ASIAEGGRQCGLSMQDAILLSAQTMLGAATMVLNGEKTPEELIREVTTPGGTTEAGLKQM 241 Query: 251 EKAGFRGILMNAVVAAAKRSQEL 273 + R ++ V AAA RS EL Sbjct: 242 DAHHVRQAMIETVKAAAARSNEL 264 Lambda K H 0.315 0.131 0.362 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: 151 Number of extensions: 11 Number of successful extensions: 3 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: 274 Length of database: 266 Length adjustment: 25 Effective length of query: 249 Effective length of database: 241 Effective search space: 60009 Effective search space used: 60009 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_012506656.1 PAES_RS10560 (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.9684.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-80 256.3 6.7 2e-80 256.2 6.7 1.0 1 lcl|NCBI__GCF_000020625.1:WP_012506656.1 PAES_RS10560 pyrroline-5-carboxy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020625.1:WP_012506656.1 PAES_RS10560 pyrroline-5-carboxylate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 256.2 6.7 2e-80 2e-80 1 263 [] 6 264 .. 6 264 .. 0.98 Alignments for each domain: == domain 1 score: 256.2 bits; conditional E-value: 2e-80 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 i+++G G++++al+sgl++ +++i+ +++ ++++aa +k++g+e ts+a+e++++a +++lavKP lcl|NCBI__GCF_000020625.1:WP_012506656.1 6 IGFVGTGRIARALISGLVND---PANRICGYDKDPDAIAAVVKQFGIEGTSSAAEVARDARIIILAVKP 71 89*****************8...4789****************************************** PP TIGR00112 70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138 +++ ev++el+ + t ++lliS++AG+t e ++q+ + rv+RvmPNt+a g+g+ta++++ ++++ lcl|NCBI__GCF_000020625.1:WP_012506656.1 72 YQIGEVVEELRP-HLTTGHLLISVAAGITSEFIRQHSIDAMRVIRVMPNTPAFTGQGMTALSKGIMATQ 139 ***********9.7889******************99999***************************** PP TIGR00112 139 eqkelveellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkG 207 e+ +l++ +++a+G v ++e+l+da+ta+sGSgPA++f li ++a++g ++GL+++ a l+aqt+ G lcl|NCBI__GCF_000020625.1:WP_012506656.1 140 EDIALATTMFSAIGRVAVLDERLMDAATAVSGSGPAYMFSLIASIAEGGRQCGLSMQDAILLSAQTMLG 208 ********************************************************************* PP TIGR00112 208 aaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263 aa+++ + +++p++L+ +Vt+PgGtT agl+ + +++vr+a+ie+v+aa++rs+eL lcl|NCBI__GCF_000020625.1:WP_012506656.1 209 AATMVLNGEKTPEELIREVTTPGGTTEAGLKQMDAHHVRQAMIETVKAAAARSNEL 264 *****************************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (263 nodes) Target sequences: 1 (266 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: 10.63 // [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