GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PRO3 in Escherichia coli BW25113

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.372.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.22
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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