Align pyrroline-5-carboxylate reductase (characterized)
to candidate 14524 b0386 pyrroline-5-carboxylate reductase (NCBI)
Query= CharProtDB::CH_024367 (269 letters) >FitnessBrowser__Keio:14524 Length = 269 Score = 522 bits (1344), Expect = e-153 Identities = 269/269 (100%), Positives = 269/269 (100%) Query: 1 MEKKIGFIGCGNMGKAILGGLIASGQVLPGQIWVYTPSPDKVAALHDQFGINAAESAQEV 60 MEKKIGFIGCGNMGKAILGGLIASGQVLPGQIWVYTPSPDKVAALHDQFGINAAESAQEV Sbjct: 1 MEKKIGFIGCGNMGKAILGGLIASGQVLPGQIWVYTPSPDKVAALHDQFGINAAESAQEV 60 Query: 61 AQIADIIFAAVKPGIMIKVLSEITSSLNKDSLVVSIAAGVTLDQLARALGHDRKIIRAMP 120 AQIADIIFAAVKPGIMIKVLSEITSSLNKDSLVVSIAAGVTLDQLARALGHDRKIIRAMP Sbjct: 61 AQIADIIFAAVKPGIMIKVLSEITSSLNKDSLVVSIAAGVTLDQLARALGHDRKIIRAMP 120 Query: 121 NTPALVNAGMTSVTPNALVTPEDTADVLNIFRCFGEAEVIAEPMIHPVVGVSGSSPAYVF 180 NTPALVNAGMTSVTPNALVTPEDTADVLNIFRCFGEAEVIAEPMIHPVVGVSGSSPAYVF Sbjct: 121 NTPALVNAGMTSVTPNALVTPEDTADVLNIFRCFGEAEVIAEPMIHPVVGVSGSSPAYVF 180 Query: 181 MFIEAMADAAVLGGMPRAQAYKFAAQAVMGSAKMVLETGEHPGALKDMVCSPGGTTIEAV 240 MFIEAMADAAVLGGMPRAQAYKFAAQAVMGSAKMVLETGEHPGALKDMVCSPGGTTIEAV Sbjct: 181 MFIEAMADAAVLGGMPRAQAYKFAAQAVMGSAKMVLETGEHPGALKDMVCSPGGTTIEAV 240 Query: 241 RVLEEKGFRAAVIEAMTKCMEKSEKLSKS 269 RVLEEKGFRAAVIEAMTKCMEKSEKLSKS Sbjct: 241 RVLEEKGFRAAVIEAMTKCMEKSEKLSKS 269 Lambda K H 0.318 0.133 0.374 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: 423 Number of extensions: 11 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: 269 Length of database: 269 Length adjustment: 25 Effective length of query: 244 Effective length of database: 244 Effective search space: 59536 Effective search space used: 59536 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate 14524 b0386 (pyrroline-5-carboxylate reductase (NCBI))
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.17430.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-97 309.8 4.0 9.8e-97 309.7 4.0 1.0 1 lcl|FitnessBrowser__Keio:14524 b0386 pyrroline-5-carboxylate re Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:14524 b0386 pyrroline-5-carboxylate reductase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 309.7 4.0 9.8e-97 9.8e-97 1 263 [] 5 266 .. 5 266 .. 0.99 Alignments for each domain: == domain 1 score: 309.7 bits; conditional E-value: 9.8e-97 TIGR00112 1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdleevlael 79 i++iG+Gnmg+a+l gl+++g+ + +i+v+++s++k+aal++++g++++++a+e+++ ad+++ avKP + +vl+e+ lcl|FitnessBrowser__Keio:14524 5 IGFIGCGNMGKAILGGLIASGQVLPGQIWVYTPSPDKVAALHDQFGINAAESAQEVAQIADIIFAAVKPGIMIKVLSEI 83 89****************************************************************************9 PP TIGR00112 80 kseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveellkavGkvveve 158 +s + +k++l++Si+AGvt+++l ++l+++++++R+mPNt+a v+ag+t+++ ++ v++e+++ v ++++++G++ ++ lcl|FitnessBrowser__Keio:14524 84 TS-SLNKDSLVVSIAAGVTLDQLARALGHDRKIIRAMPNTPALVNAGMTSVTPNALVTPEDTADVLNIFRCFGEAEVIA 161 99.7779************************************************************************ PP TIGR00112 159 eklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalLkdkVtsPgGtTiagl 237 e +++ v+++sGS+PA+vf++iea+ada+v G+pr++a+++aaq+++G+ak++ e+gehp +Lkd V+sPgGtTi+++ lcl|FitnessBrowser__Keio:14524 162 EPMIHPVVGVSGSSPAYVFMFIEAMADAAVLGGMPRAQAYKFAAQAVMGSAKMVLETGEHPGALKDMVCSPGGTTIEAV 240 ******************************************************************************* PP TIGR00112 238 avLeekgvrsavieaveaavkrseeL 263 +vLeekg+r+aviea+++++++se+L lcl|FitnessBrowser__Keio:14524 241 RVLEEKGFRAAVIEAMTKCMEKSEKL 266 ***********************997 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 7.26 // [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