Alignments for a candidate for hcs in Denitrovibrio acetiphilus DSM 12809

GapMind for Amino acid biosynthesis

Alignments for a candidate for hcs in Denitrovibrio acetiphilus DSM 12809

Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_013010361.1 DACET_RS05300 homocitrate synthase

Query= BRENDA::P58637
         (376 letters)



>NCBI__GCF_000025725.1:WP_013010361.1
          Length = 376

 Score =  340 bits (871), Expect = 5e-98
 Identities = 171/363 (47%), Positives = 239/363 (65%)

Query: 4   VLINDTTLRDGEQAAGVAFSVEEKIAIAKFLDAIGVHEIEVGIPAMGKAEQEAIANIVKL 63
           ++I+DTTLRDGEQ  GVAFS +EK+ I K LDAIGV EIE GIP MG AE     +I++L
Sbjct: 1   MIIDDTTLRDGEQTPGVAFSRKEKLTIVKHLDAIGVQEIEAGIPVMGLAESRMFESIMEL 60

Query: 64  DLSANLLGWNRAVIADIQASIACGLQRVHISIPVSAIQIAVKFHGQWQVVLQKLHDSISF 123
            L A ++ WNRA+I D+QASIA G   + IS+P+S +QI  K +     +L ++   + F
Sbjct: 61  GLDARIIAWNRALIGDVQASIAAGANSIEISLPMSDVQINTKLNKTRGWILDQVKSVLDF 120

Query: 124 AVDQGLFVSIGGEDSSRAEESFLLDVVLAAQEWGASRFRFCDTVGILDPFTTHAKVKQLV 183
             +  L++S+GGED+SRA+  FL + +   +  GA RFRFCDTVGILDPF T+    ++ 
Sbjct: 121 CANHDLYISVGGEDASRADFDFLAEYIRTIEAHGADRFRFCDTVGILDPFKTYELTAKIR 180

Query: 184 ASLTIPVEMHTHNDFGLATANALAGTKAGALSVNTTVNGLGERAGNAALEEVVMALKHLY 243
              ++ +E+HTHNDFG+ATANALA  +AGA  VNTTV GLGERAGNA LEE++MA +H+Y
Sbjct: 181 EITSMDIEIHTHNDFGMATANALAAVRAGATHVNTTVIGLGERAGNAPLEEIIMASRHVY 240

Query: 244 HHDLGIDTRRLLEISQLVASASGHPVPPWKAIVGENTFAHESGIHAHGVLQNPQTYEPFA 303
             D   DT+ +  +S+ VA A+G  + P + ++GE  F HESGIH  GVL+NP+ YE F 
Sbjct: 241 GMDDAFDTKTMRSLSEYVAQAAGRNLDPQRPVIGEFMFTHESGIHTDGVLKNPKNYEAFD 300

Query: 304 PEEVGRERRLVVGKHSGRHLLSSILQQHDIILNHEETQFVLDAVRQESVEKKRSLTDQEL 363
           P E+  +R LV G  SG  +L  IL+Q  I+L   +   +L   ++ + + K  L   ++
Sbjct: 301 PAELNMQRNLVFGNQSGLAVLKYILEQEGIVLESYQLTGLLHEAKKLARKNKAVLNKAQV 360

Query: 364 LHL 366
           + L
Sbjct: 361 IGL 363


Lambda     K      H
   0.319    0.133    0.383 

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: 377
Number of extensions: 14
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: 376
Length of database: 376
Length adjustment: 30
Effective length of query: 346
Effective length of database: 346
Effective search space:   119716
Effective search space used:   119716
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_013010361.1 DACET_RS05300 (homocitrate synthase)
to HMM TIGR02660 (nifV: homocitrate synthase (EC 2.3.3.14))

# 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/TIGR02660.hmm
# target sequence database:        /tmp/gapView.2927167.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02660  [M=365]
Accession:   TIGR02660
Description: nifV_homocitr: homocitrate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.9e-145  469.1   0.3   6.6e-145  468.9   0.3    1.0  1  NCBI__GCF_000025725.1:WP_013010361.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025725.1:WP_013010361.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.9   0.3  6.6e-145  6.6e-145       3     364 ..       2     363 ..       1     364 [. 0.99

  Alignments for each domain:
  == domain 1  score: 468.9 bits;  conditional E-value: 6.6e-145
                             TIGR02660   3 linDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaalglkarllaWcRlra 75 
                                           +i+DttLRDGEq++gvaFs++EKl i k Ld++Gv+e+E+Gip mg +E ++ + i++lgl+ar++aW+R+  
  NCBI__GCF_000025725.1:WP_013010361.1   2 IIDDTTLRDGEQTPGVAFSRKEKLTIVKHLDAIGVQEIEAGIPVMGLAESRMFESIMELGLDARIIAWNRALI 74 
                                           89*********************************************************************** PP

                             TIGR02660  76 edieaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDasRadeeflvela 148
                                            d++a+ ++G +++++s+p+sd+q+++kl+k+r w+l+++k+++ +  ++ l++svg+eDasRad +fl+e +
  NCBI__GCF_000025725.1:WP_013010361.1  75 GDVQASIAAGANSIEISLPMSDVQINTKLNKTRGWILDQVKSVLDFCANHDLYISVGGEDASRADFDFLAEYI 147
                                           ************************************************************************* PP

                             TIGR02660 149 evakeagakRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntlaavkaGassvsvtvlGl 221
                                           +++++ ga+R+Rf+Dtvg+ldPf+tyel +++r+ +++++E+H+HnD+G+AtAn+laav+aGa++v++tv+Gl
  NCBI__GCF_000025725.1:WP_013010361.1 148 RTIEAHGADRFRFCDTVGILDPFKTYELTAKIREITSMDIEIHTHNDFGMATANALAAVRAGATHVNTTVIGL 220
                                           ************************************************************************* PP

                             TIGR02660 222 GERAGnAaleevalalkellgldtgidlselkelsqlvakasgraleaqkavvGesvFaHEsGiHvdgllkde 294
                                           GERAGnA+lee+++a ++++g+d   d++++++ls++va+a+gr+l++q++v+Ge +F+HEsGiH dg+lk++
  NCBI__GCF_000025725.1:WP_013010361.1 221 GERAGNAPLEEIIMASRHVYGMDDAFDTKTMRSLSEYVAQAAGRNLDPQRPVIGEFMFTHESGIHTDGVLKNP 293
                                           ************************************************************************* PP

                             TIGR02660 295 atYesldPeevGrerelviGKHsgraaviealkelgleleeeeaeelleavravaerlKrsleeeelaal 364
                                           ++Ye++dP+e+ ++r+lv G  sg a ++  l++ g+ le+ +++ ll++ ++ a ++K  l++++++ l
  NCBI__GCF_000025725.1:WP_013010361.1 294 KNYEAFDPAELNMQRNLVFGNQSGLAVLKYILEQEGIVLESYQLTGLLHEAKKLARKNKAVLNKAQVIGL 363
                                           *************************************************************999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (376 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.17
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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