Alignments for a candidate for proC in Desulfovibrio gracilis DSM 16080

GapMind for Amino acid biosynthesis

Alignments for a candidate for proC in Desulfovibrio gracilis DSM 16080

Align pyrroline-5-carboxylate reductase (EC 1.5.1.2) (characterized)
to candidate WP_078715724.1 B5D49_RS00655 pyrroline-5-carboxylate reductase

Query= reanno::DvH:207819
         (265 letters)



>NCBI__GCF_900167125.1:WP_078715724.1
          Length = 263

 Score =  216 bits (550), Expect = 4e-61
 Identities = 117/260 (45%), Positives = 165/260 (63%), Gaps = 1/260 (0%)

Query: 5   LGCIGCGNMGSAILRGLSGREGLRLVGCDPTGAKLAALAD-AGVEGVADIAAAVRASDIV 63
           +G IG GNMG+AI+  LSG EG+ L G + T +KL  LA   G+    D+      SD V
Sbjct: 3   IGFIGTGNMGAAIIEALSGMEGITLYGVNRTRSKLEELAARTGLIPCGDVRELTEKSDFV 62

Query: 64  LVAVKPGQVGAVLGAAMPELDSGKVVVSIASGVSVGSLREMSGGRCPVVRVMPNTPAMVG 123
           ++AVKP QVG V  A +P L S K ++SIA+G+++ SL++  G  CPV+RVMP TP +V 
Sbjct: 63  VLAVKPQQVGEVWPAMVPALSSDKCMISIAAGLTLESLQQSIGHACPVIRVMPITPVLVK 122

Query: 124 AGVFALCFEDATLDEVRRTLVKELFEALGRVLVLPEEKFNAFTAVVGCGPAYVFHFMEAV 183
            GV A+C +D TL + ++  V+ +F   G V ++ E  F+ FTA++G GPA +FH ME +
Sbjct: 123 EGVTAVCLDDKTLTQEQKDAVQRIFSPSGDVHIVAENLFDVFTALIGSGPALLFHLMETL 182

Query: 184 VEAAVTLGFPRHEATDMVVDLFAGSVKLAATSGTHLSLLREAVCSPAGNTIAAMNQFDRD 243
           +E+ V LG  R  A+ MV  LF G+  +A  S  H+SLL+E   +PAG T AA+  F+R 
Sbjct: 183 IESGVELGIERAAASRMVKKLFRGAGIMAEQSEQHISLLKEMSIAPAGTTNAALAHFERT 242

Query: 244 AVRGRIIDAILAAYRRGQEM 263
           A+RG I+DAI  AY R  E+
Sbjct: 243 AIRGNIMDAIRKAYERSIEL 262


Lambda     K      H
   0.322    0.137    0.393 

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: 170
Number of extensions: 10
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: 265
Length of database: 263
Length adjustment: 25
Effective length of query: 240
Effective length of database: 238
Effective search space:    57120
Effective search space used:    57120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate WP_078715724.1 B5D49_RS00655 (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.9488.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      1e-73  234.2   1.3    1.2e-73  234.0   1.3    1.0  1  lcl|NCBI__GCF_900167125.1:WP_078715724.1  B5D49_RS00655 pyrroline-5-carbox


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900167125.1:WP_078715724.1  B5D49_RS00655 pyrroline-5-carboxylate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.0   1.3   1.2e-73   1.2e-73       1     263 []       3     262 ..       3     262 .. 0.97

  Alignments for each domain:
  == domain 1  score: 234.0 bits;  conditional E-value: 1.2e-73
                                 TIGR00112   1 iaiiGaGnmgeallsgllkkgakakkeilvierseeklaalakelgvevtsdaeeavkeadvvllavKP 69 
                                               i++iG Gnmg+a++++l+  + +    ++ ++r  +kl++la+++g   + d++e+ +++d+v+lavKP
  lcl|NCBI__GCF_900167125.1:WP_078715724.1   3 IGFIGTGNMGAAIIEALSGMEGI---TLYGVNRTRSKLEELAARTGLIPCGDVRELTEKSDFVVLAVKP 68 
                                               89**************9987555...79999999*********************************** PP

                                 TIGR00112  70 qdleevlaelkseektkeklliSilAGvtiekleqlleaekrvvRvmPNtaakvgagvtaiaassevse 138
                                               q++ ev   +     + +k++iSi+AG+t+e l+q +++ ++v+RvmP t++ v++gvta++ ++++  
  lcl|NCBI__GCF_900167125.1:WP_078715724.1  69 QQVGEVWPAMVP-ALSSDKCMISIAAGLTLESLQQSIGHACPVIRVMPITPVLVKEGVTAVCLDDKTLT 136
                                               ********9988.7779*********************************************9988777 PP

                                 TIGR00112 139 e.qkelveellkavGkvveveeklldavtalsGSgPAfvflliealadagvklGLpreeakelaaqtlk 206
                                               + qk+ v+++++  G+v+ v+e+l+d +tal GSgPA +f+l+e l+++gv+lG++r+ a +++++++ 
  lcl|NCBI__GCF_900167125.1:WP_078715724.1 137 QeQKDAVQRIFSPSGDVHIVAENLFDVFTALIGSGPALLFHLMETLIESGVELGIERAAASRMVKKLFR 205
                                               66******************************************************************* PP

                                 TIGR00112 207 GaaklleesgehpalLkdkVtsPgGtTiaglavLeekgvrsavieaveaavkrseeL 263
                                               Ga+ + e+s++h +lLk+  + P+GtT a+la +e+ ++r+ +++a+++a++rs eL
  lcl|NCBI__GCF_900167125.1:WP_078715724.1 206 GAGIMAEQSEQHISLLKEMSIAPAGTTNAALAHFERTAIRGNIMDAIRKAYERSIEL 262
                                               *****************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (263 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: 9.85
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis