Alignments for a candidate for leuA in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Dechlorosoma suillum PS

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate Dsui_3519 Dsui_3519 2-isopropylmalate synthase, bacterial type

Query= BRENDA::Q9JZG1
         (517 letters)



>FitnessBrowser__PS:Dsui_3519
          Length = 513

 Score =  712 bits (1839), Expect = 0.0
 Identities = 358/508 (70%), Positives = 426/508 (83%)

Query: 6   RVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAIAK 65
           ++IIFDTTLRDGEQSPGA+MTKEEK+RVARQLE++ VD+IEAGFAAASPGDF+A++AIA+
Sbjct: 4   QLIIFDTTLRDGEQSPGASMTKEEKLRVARQLERMRVDVIEAGFAAASPGDFDAIHAIAE 63

Query: 66  TITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEAAV 125
            I  STVCSL+RA E DIR+AGEA+ PA + RIHTFIATSPIHME KL+M P QV+E AV
Sbjct: 64  AIKDSTVCSLARANENDIRRAGEAIKPAARGRIHTFIATSPIHMEKKLRMSPDQVVEQAV 123

Query: 126 KAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTEEF 185
           KA+  AREYT+DVEFS EDA RSEIDFL  I  AVI+AGATTIN+PDTVGY++P +  E 
Sbjct: 124 KAIGWAREYTNDVEFSAEDAGRSEIDFLCRIFEAVIKAGATTINVPDTVGYNLPSQFAET 183

Query: 186 FRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNASVEE 245
            R+LI + P   KVVWS HCHNDLGLAVANSLAA+  GARQVECT+NGLGERAGNAS+EE
Sbjct: 184 IRQLIERVPGADKVVWSVHCHNDLGLAVANSLAAVLAGARQVECTINGLGERAGNASLEE 243

Query: 246 IVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIHQDG 305
           +VMA + R D+F +ET +DTTQIVP+SKLVS ITGYPVQPNKAIVGANAF+HESGIHQDG
Sbjct: 244 VVMATRTRADIFPVETRVDTTQIVPASKLVSQITGYPVQPNKAIVGANAFAHESGIHQDG 303

Query: 306 VLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFARFKE 365
           VLKHRETYEIM AE VGW+ N+L LGK SGRNAFKT+LA+LGI+L SEEALNAAFARFKE
Sbjct: 304 VLKHRETYEIMRAEDVGWSQNKLVLGKHSGRNAFKTRLAELGIDLPSEEALNAAFARFKE 363

Query: 366 LADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGEEKRAS 425
           LADKK EIFDEDL ALVSDE  +   E YK +  ++ +ETGE P + +  ++ G E +A+
Sbjct: 364 LADKKHEIFDEDLQALVSDETVTPEQEHYKLVYSQVCSETGEIPESAVTLAVGGAEHKAA 423

Query: 426 ATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQGADT 485
           ++GSGPVDA FKAIE +A SGA   +YSVNA+T GT++QGE +VRLA+G R+VNGQGADT
Sbjct: 424 SSGSGPVDATFKAIEKIAASGAEQLLYSVNAITTGTDAQGEVTVRLAKGGRIVNGQGADT 483

Query: 486 DVLVATAKAYLSALSKLEFSAAKPKAQG 513
           D+++A+AKAYL+AL+KL  S  K   QG
Sbjct: 484 DIVIASAKAYLNALNKLHSSLEKLNPQG 511


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: 747
Number of extensions: 20
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: 517
Length of database: 513
Length adjustment: 35
Effective length of query: 482
Effective length of database: 478
Effective search space:   230396
Effective search space used:   230396
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 Dsui_3519 Dsui_3519 (2-isopropylmalate synthase, bacterial type)
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.17438.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-226  737.8   4.5   2.9e-226  737.6   4.5    1.0  1  lcl|FitnessBrowser__PS:Dsui_3519  Dsui_3519 2-isopropylmalate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3519  Dsui_3519 2-isopropylmalate synthase, bacterial type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  737.6   4.5  2.9e-226  2.9e-226       2     494 .]       5     498 ..       4     498 .. 0.99

  Alignments for each domain:
  == domain 1  score: 737.6 bits;  conditional E-value: 2.9e-226
                         TIGR00973   2 vlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravekdi 78 
                                       ++ifdttlrdGeq+pgas+t eekl++a++ler+ vd+ieaGf+++s+gdf+a++ ia+++k+++v++lara e+di
  lcl|FitnessBrowser__PS:Dsui_3519   5 LIIFDTTLRDGEQSPGASMTKEEKLRVARQLERMRVDVIEAGFAAASPGDFDAIHAIAEAIKDSTVCSLARANENDI 81 
                                       79*************************************************************************** PP

                         TIGR00973  79 daaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvveaa 155
                                         a ea+kpa++ rihtfiats+ih+e+kl+++ d+v+e++vka+ +a+++++dvefsaedagr+e++fl+r++ea+
  lcl|FitnessBrowser__PS:Dsui_3519  82 RRAGEAIKPAARGRIHTFIATSPIHMEKKLRMSPDQVVEQAVKAIGWAREYTNDVEFSAEDAGRSEIDFLCRIFEAV 158
                                       ***************************************************************************** PP

                         TIGR00973 156 ieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinGiGer 232
                                       i+aGattin+PdtvGy lP++++e i++l e+vP+ dk++ svhch+dlGlavanslaav +GarqvectinG+Ger
  lcl|FitnessBrowser__PS:Dsui_3519 159 IKAGATTINVPDTVGYNLPSQFAETIRQLIERVPGADKVVWSVHCHNDLGLAVANSLAAVLAGARQVECTINGLGER 235
                                       ***************************************************************************** PP

                         TIGR00973 233 aGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknketye 309
                                       aGna+leevvma ++r d+++vet ++t +i  +s+lvs++tg +vq+nkaivG+nafahesGihqdGvlk++etye
  lcl|FitnessBrowser__PS:Dsui_3519 236 AGNASLEEVVMATRTRADIFPVETRVDTTQIVPASKLVSQITGYPVQPNKAIVGANAFAHESGIHQDGVLKHRETYE 312
                                       ***************************************************************************** PP

                         TIGR00973 310 ilspesiGlkkeklvlgkrsGraalkkrleelGfkl.deeeldklfekfkeladkkkevfdedlealvleelrqeee 385
                                       i+++e++G +++klvlgk+sGr+a+k+rl+elG++l +ee l+ +f +fkeladkk+e+fdedl+alv++e++++e+
  lcl|FitnessBrowser__PS:Dsui_3519 313 IMRAEDVGWSQNKLVLGKHSGRNAFKTRLAELGIDLpSEEALNAAFARFKELADKKHEIFDEDLQALVSDETVTPEQ 389
                                       ***********************************945677************************************ PP

                         TIGR00973 386 eklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevk 462
                                       e++kl++ qv s + ++p ++v+l+v g+e++aa++G+Gpvda++kaieki     + l ys++a ++g+da+gev+
  lcl|FitnessBrowser__PS:Dsui_3519 390 EHYKLVYSQVCSETGEIPESAVTLAVGGAEHKAASSGSGPVDATFKAIEKIAASGAEQLLYSVNAITTGTDAQGEVT 466
                                       ***************************************************************************** PP

                         TIGR00973 463 vvlelngkkysGrgvatdiveasakayvnaln 494
                                       v+l   g+ ++G+g++tdiv asakay+naln
  lcl|FitnessBrowser__PS:Dsui_3519 467 VRLAKGGRIVNGQGADTDIVIASAKAYLNALN 498
                                       *******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (513 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.89
//
[ok]

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

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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
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