Alignments for a candidate for leuA in Denitrovibrio acetiphilus DSM 12809

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Denitrovibrio acetiphilus DSM 12809

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_013009813.1 DACET_RS02375 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>NCBI__GCF_000025725.1:WP_013009813.1
          Length = 519

 Score =  509 bits (1310), Expect = e-148
 Identities = 266/502 (52%), Positives = 362/502 (72%), Gaps = 10/502 (1%)

Query: 6   RVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAIAK 65
           RVIIFDTTLRDGEQ+PG +M  +EKI++A QLE+LGVD++EAGF  +SPGDFEAV  +AK
Sbjct: 5   RVIIFDTTLRDGEQAPGFSMNTDEKIQLALQLERLGVDVMEAGFPISSPGDFEAVTRVAK 64

Query: 66  TITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEAAV 125
            I  S V  L RA E+DI    +A+  A + RIHTFIATS IH+++KLK   ++ +E AV
Sbjct: 65  VIKNSGVAGLCRANEKDISVGWDALQHAVRPRIHTFIATSDIHLQHKLKKTREEALEIAV 124

Query: 126 KAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTEEF 185
           KAVK AR   DDVEFS EDA+RS++D+L ++  AVI AGA T+N+PDTVGY +P++ ++ 
Sbjct: 125 KAVKFARNLCDDVEFSAEDAMRSDVDYLCQVVEAVIAAGANTVNLPDTVGYKMPFEIDKV 184

Query: 186 FRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNASVEE 245
             E+I + PN  K   S HCHNDLGL+VANSL A+  GA Q+ECT+NG+GERAGN S+EE
Sbjct: 185 ISEVINRVPNVDKARISVHCHNDLGLSVANSLMAVNAGASQIECTINGIGERAGNCSLEE 244

Query: 246 IVMALKVRHDLF-GLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIHQD 304
           +VM L VR D+F  +E G+ T +I  +SK+++TITG  VQPNKAIVG NAF+HE+GIHQD
Sbjct: 245 VVMGLTVRKDVFDDIEIGVKTNEIYRASKMLTTITGVGVQPNKAIVGKNAFAHEAGIHQD 304

Query: 305 GVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFARFK 364
           G+LK+R TYEIM+ ESVG+ +  L LGK SGR+AF  ++ DLG E+E+ +A+ +AF  FK
Sbjct: 305 GMLKNRTTYEIMTPESVGYPSTSLVLGKHSGRHAFVQRIKDLGYEIEN-DAMQSAFDEFK 363

Query: 365 ELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEE--PRADIVFSIK-GEE 421
            LADKK+E+FDED+ +++ ++      E + ++ + ++  +G+   P A I  + K G E
Sbjct: 364 ILADKKKEVFDEDIESIIFNQ---AKDEQFAYVMESVNILSGDTAIPTATIKLADKDGNE 420

Query: 422 KRASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGET--SVRLARGNRVVN 479
              ++TG GPVDA+ KAIE +A  G  L+ Y + A+T G ++QGE   S         V 
Sbjct: 421 FVDASTGDGPVDAVMKAIERIAGVGGKLKSYQIKALTAGKDAQGEVVLSAEFEECGYDVR 480

Query: 480 GQGADTDVLVATAKAYLSALSK 501
           G+G+DTDV+VA+AKAYL AL+K
Sbjct: 481 GRGSDTDVVVASAKAYLDALNK 502


Lambda     K      H
   0.313    0.129    0.352 

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: 656
Number of extensions: 21
Number of successful extensions: 5
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: 517
Length of database: 519
Length adjustment: 35
Effective length of query: 482
Effective length of database: 484
Effective search space:   233288
Effective search space used:   233288
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: 52 (24.6 bits)

Align candidate WP_013009813.1 DACET_RS02375 (2-isopropylmalate synthase)
to HMM TIGR00973 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

# 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/TIGR00973.hmm
# target sequence database:        /tmp/gapView.108547.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00973  [M=494]
Accession:   TIGR00973
Description: leuA_bact: 2-isopropylmalate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-223  727.8   9.2     3e-223  727.6   9.2    1.0  1  NCBI__GCF_000025725.1:WP_013009813.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025725.1:WP_013009813.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  727.6   9.2    3e-223    3e-223       1     494 []       5     501 ..       5     501 .. 0.98

  Alignments for each domain:
  == domain 1  score: 727.6 bits;  conditional E-value: 3e-223
                             TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglara 73 
                                           rv+ifdttlrdGeqapg+s++++ek+q+a++lerlgvd++eaGfp+ss+gdfeav ++a+ +kn+ v+gl+ra
  NCBI__GCF_000025725.1:WP_013009813.1   5 RVIIFDTTLRDGEQAPGFSMNTDEKIQLALQLERLGVDVMEAGFPISSPGDFEAVTRVAKVIKNSGVAGLCRA 77 
                                           79*********************************************************************** PP

                             TIGR00973  74 vekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrtele 146
                                            ekdi + ++al+ a + rihtfiatsdihl++klkkt++e le++vkavk+a+n+ ddvefsaeda r++++
  NCBI__GCF_000025725.1:WP_013009813.1  78 NEKDISVGWDALQHAVRPRIHTFIATSDIHLQHKLKKTREEALEIAVKAVKFARNLCDDVEFSAEDAMRSDVD 150
                                           ************************************************************************* PP

                             TIGR00973 147 flarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGa 219
                                           +l++vvea+i aGa t+n+PdtvGy +P e  ++i+e+ ++vPn+dka +svhch+dlGl+vansl av++Ga
  NCBI__GCF_000025725.1:WP_013009813.1 151 YLCQVVEAVIAAGANTVNLPDTVGYKMPFEIDKVISEVINRVPNVDKARISVHCHNDLGLSVANSLMAVNAGA 223
                                           ************************************************************************* PP

                             TIGR00973 220 rqvectinGiGeraGnaaleevvmalkvrkdfln.vetgintkeiyrtsrlvskltgmlvqrnkaivGdnafa 291
                                           +q+ectinGiGeraGn++leevvm l vrkd+++ +e+g++t+eiyr+s++++ +tg+ vq+nkaivG+nafa
  NCBI__GCF_000025725.1:WP_013009813.1 224 SQIECTINGIGERAGNCSLEEVVMGLTVRKDVFDdIEIGVKTNEIYRASKMLTTITGVGVQPNKAIVGKNAFA 296
                                           *********************************989************************************* PP

                             TIGR00973 292 hesGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkk 364
                                           he+GihqdG+lkn++tyei++pes+G  ++ lvlgk+sGr+a+ +r+++lG++++++ ++ +f++fk ladkk
  NCBI__GCF_000025725.1:WP_013009813.1 297 HEAGIHQDGMLKNRTTYEIMTPESVGYPSTSLVLGKHSGRHAFVQRIKDLGYEIENDAMQSAFDEFKILADKK 369
                                           ************************************************************************* PP

                             TIGR00973 365 kevfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvk.geekeaaatGnGpvdavykaieki 436
                                           kevfded+e++++++ + +e+  + +e++++ sg++ +ptat+kl+ k g+e  +a+tG Gpvdav+kaie+i
  NCBI__GCF_000025725.1:WP_013009813.1 370 KEVFDEDIESIIFNQAK-DEQFAYVMESVNILSGDTAIPTATIKLADKdGNEFVDASTGDGPVDAVMKAIERI 441
                                           **************998.66777**********************99879999******************** PP

                             TIGR00973 437 lelevklleysitakgegkdalgevkvvleln..gkkysGrgvatdiveasakayvnaln 494
                                            ++  kl+ y+i+a + gkda+gev + +e++  g  + Grg +td+v asakay++aln
  NCBI__GCF_000025725.1:WP_013009813.1 442 AGVGGKLKSYQIKALTAGKDAQGEVVLSAEFEecGYDVRGRGSDTDVVVASAKAYLDALN 501
                                           ***************************999873367789********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (519 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: 00:00:00.01
# Mc/sec: 18.97
//
[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