Alignments for a candidate for PRO3 in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for PRO3 in Echinicola vietnamensis KMM 6221, DSM 17526

Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate Echvi_2479 Echvi_2479 pyrroline-5-carboxylate reductase

Query= SwissProt::Q9HH99
         (270 letters)



>FitnessBrowser__Cola:Echvi_2479
          Length = 265

 Score =  157 bits (396), Expect = 3e-43
 Identities = 89/264 (33%), Positives = 149/264 (56%), Gaps = 3/264 (1%)

Query: 1   MENQKIGFIGAGKMGSALMQGTIKAGIVTPENIGASDVYEPFLKDLQAKLGIRVSTDNAV 60
           M+N KI  IG G +G +++ G ++      +N+  +  +   L  LQ+ LG+ V+ DN  
Sbjct: 1   MKNLKIAIIGCGNLGLSIVNGLLETEGFEAKNLMVTKRHPENLSHLQS-LGVTVTADNKS 59

Query: 61  IVRESDILILAVKPQTLSSVLSNLKNEITSEK-LVISIAAGVPLSTYEDALLEGTRVVRV 119
             + +D++IL VKP  +  +L  +   ++ +K  +IS+A GV L      L   T + R 
Sbjct: 60  AAKAADLVILGVKPYNIPHILKEIAPVVSPDKQTIISLATGVTLEEMYQHLPSTTALYRA 119

Query: 120 MPNIAATVSEAASGIAPGKNATPEDLKAALEIFSAVGTAVQVPESLMDAVTGLSGSGPAF 179
           MPNIAA + E+ + I  G+N+TPE+      +F+++G ++ + E LM+A T L   G A+
Sbjct: 120 MPNIAADIQESITCIC-GQNSTPENEDIIKALFNSIGISIIIEEHLMEAATVLGACGIAY 178

Query: 180 IFPVIEAMADGAVLEGMDRKSALTLAAQTVLGAAKMALETGMHPGELKDMVTSPAGTTIQ 239
           +   + AM  G +  G D K+A T+  QTV GAA++ ++ G+HP    D VT+P G TI 
Sbjct: 179 VLRFMRAMTQGGIQIGFDAKTANTIVNQTVKGAAELLIKKGIHPEAAIDKVTTPKGCTIV 238

Query: 240 GIHSLEEAGIRAAFMNAVIRASER 263
           G++ +E  G  AA +  V+ + E+
Sbjct: 239 GLNEMEHHGFSAAMVKGVLASYEK 262


Lambda     K      H
   0.313    0.130    0.343 

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: 7
Number of successful extensions: 4
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: 270
Length of database: 265
Length adjustment: 25
Effective length of query: 245
Effective length of database: 240
Effective search space:    58800
Effective search space used:    58800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate Echvi_2479 Echvi_2479 (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.16368.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
      9e-73  231.1   4.1      1e-72  230.9   4.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2479  Echvi_2479 pyrroline-5-carboxyla


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2479  Echvi_2479 pyrroline-5-carboxylate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.9   4.1     1e-72     1e-72       1     260 [.       6     263 ..       6     265 .] 0.97

  Alignments for each domain:
  == domain 1  score: 230.9 bits;  conditional E-value: 1e-72
                            TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKPqdlee 74 
                                          iaiiG+Gn+g ++++gll+++  ++k+++v++r++e+l  ++++lgv+vt+d+++a+k+ad+v+l+vKP+++++
  lcl|FitnessBrowser__Cola:Echvi_2479   6 IAIIGCGNLGLSIVNGLLETEGFEAKNLMVTKRHPENLS-HLQSLGVTVTADNKSAAKAADLVILGVKPYNIPH 78 
                                          89*********************999**99999988876.6799****************************** PP

                            TIGR00112  75 vlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevseeqkelveell 148
                                          +l+e++   +  ++++iS++ Gvt+e+++q+l+++++++R+mPN+aa +++++t i+ + + ++e+++ +++l+
  lcl|FitnessBrowser__Cola:Echvi_2479  79 ILKEIAPVVSPDKQTIISLATGVTLEEMYQHLPSTTALYRAMPNIAADIQESITCICGQ-NSTPENEDIIKALF 151
                                          *******99999**********************************************9.5779999******* PP

                            TIGR00112 149 kavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlkGaaklleesgehpalL 222
                                          +++G  + +ee+l++a+t l ++g A+v+ ++ a+ ++g++ G+++++a++++ qt+kGaa+ll ++g hp++ 
  lcl|FitnessBrowser__Cola:Echvi_2479 152 NSIGISIIIEEHLMEAATVLGACGIAYVLRFMRAMTQGGIQIGFDAKTANTIVNQTVKGAAELLIKKGIHPEAA 225
                                          ************************************************************************** PP

                            TIGR00112 223 kdkVtsPgGtTiaglavLeekgvrsavieaveaavkrs 260
                                          +dkVt+P+G+Ti gl+++e++g+ +a+ ++v a++++ 
  lcl|FitnessBrowser__Cola:Echvi_2479 226 IDKVTTPKGCTIVGLNEMEHHGFSAAMVKGVLASYEKI 263
                                          **********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (265 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: 9.47
//
[ok]

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

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources