Alignments for a candidate for leuA in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Paraburkholderia bryophila 376MFSha3.1

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate H281DRAFT_04556 H281DRAFT_04556 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>FitnessBrowser__Burk376:H281DRAFT_04556
          Length = 515

 Score =  624 bits (1608), Expect = 0.0
 Identities = 318/513 (61%), Positives = 400/513 (77%), Gaps = 2/513 (0%)

Query: 4   TNRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAI 63
           ++++IIFDTTLRDGEQSPGA+MTKEEKIR+A+QLE++ VD+IEAGFAA+S GDF+++  I
Sbjct: 2   SDKLIIFDTTLRDGEQSPGASMTKEEKIRIAKQLERMKVDVIEAGFAASSNGDFDSIQTI 61

Query: 64  AKTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEA 123
           A  I +S VCSL+RA ++DI++A +A+ PA + RIHTFIATSP+HME KL+M P QV E 
Sbjct: 62  AGLIKESMVCSLARANDKDIQRAADALKPAERFRIHTFIATSPLHMEKKLRMTPDQVFEQ 121

Query: 124 AVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTE 183
           A  AV+ AR++TDDVEFS ED  RS++DFL  +  AVI  GATTINI DTVGY +P    
Sbjct: 122 AKLAVRFARKFTDDVEFSPEDGSRSDMDFLCRVLEAVIAEGATTINIADTVGYGVPELYG 181

Query: 184 EFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALK-GGARQVECTVNGLGERAGNAS 242
              + L  + PN  K V+S HCHNDLG+AVANSLA ++ GGARQVECT+NGLGERAGN S
Sbjct: 182 NLVKTLRERIPNSHKAVFSVHCHNDLGMAVANSLAGVQIGGARQVECTINGLGERAGNTS 241

Query: 243 VEEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIH 302
           +EEIVMA+K R D FGLE G+DTTQIVP+SKLVS ITG+ VQPNKA+VGANAF+H SGIH
Sbjct: 242 LEEIVMAVKTRKDYFGLELGLDTTQIVPASKLVSQITGFVVQPNKAVVGANAFAHASGIH 301

Query: 303 QDGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFAR 362
           QDGVLK R+TYEIM AE VGW+ N++ LGKLSGRNAFK +L +LGI L+SE  LN AFAR
Sbjct: 302 QDGVLKARDTYEIMRAEDVGWSANKIVLGKLSGRNAFKQRLQELGIALDSEAELNTAFAR 361

Query: 363 FKELADKKREIFDEDLHALVSDEMG-SMNAESYKFISQKISTETGEEPRADIVFSIKGEE 421
           FKELAD+K EIFDED+ A+V++E   +   E YKF+S    +ETGE+P A IVF++ G+E
Sbjct: 362 FKELADRKAEIFDEDIIAIVTEESAEAQQKEHYKFLSLSQHSETGEQPHAKIVFAMDGKE 421

Query: 422 KRASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQ 481
               A G+GPVDA   AIE+   SG+ L +YSVNA+T GT++QGE +VRL++  R+VNG 
Sbjct: 422 ITGEARGNGPVDATLNAIETEVGSGSELLLYSVNAITTGTQAQGEVTVRLSKSGRIVNGV 481

Query: 482 GADTDVLVATAKAYLSALSKLEFSAAKPKAQGS 514
           G D D++ A+AKAY+SAL+KL  +  K   Q S
Sbjct: 482 GTDPDIVAASAKAYISALNKLYSNVDKVNPQRS 514


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: 669
Number of extensions: 18
Number of successful extensions: 3
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: 515
Length adjustment: 35
Effective length of query: 482
Effective length of database: 480
Effective search space:   231360
Effective search space used:   231360
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 H281DRAFT_04556 H281DRAFT_04556 (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.31861.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.7e-218  711.3   6.1     3e-218  711.1   6.1    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04556  H281DRAFT_04556 2-isopropylmalat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04556  H281DRAFT_04556 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  711.1   6.1    3e-218    3e-218       1     494 []       4     500 ..       4     500 .. 0.99

  Alignments for each domain:
  == domain 1  score: 711.1 bits;  conditional E-value: 3e-218
                                    TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknar 66 
                                                  +++ifdttlrdGeq+pgas+t eek++iak+ler+ vd+ieaGf++ss+gdf+++q+ia  +k+++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04556   4 KLIIFDTTLRDGEQSPGASMTKEEKIRIAKQLERMKVDVIEAGFAASSNGDFDSIQTIAGLIKESM 69 
                                                  689*************************************************************** PP

                                    TIGR00973  67 vvglaravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvdd 132
                                                  v++lara +kdi+ aa+alkpae++rihtfiats++h+e+kl++t d+v e+++ av++a++f+dd
  lcl|FitnessBrowser__Burk376:H281DRAFT_04556  70 VCSLARANDKDIQRAADALKPAERFRIHTFIATSPLHMEKKLRMTPDQVFEQAKLAVRFARKFTDD 135
                                                  ****************************************************************** PP

                                    TIGR00973 133 vefsaedagrteleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsv 198
                                                  vefs+ed +r++++fl+rv+ea+i  Gattini dtvGy +P+ yg+l+k+l+e++Pn +ka++sv
  lcl|FitnessBrowser__Burk376:H281DRAFT_04556 136 VEFSPEDGSRSDMDFLCRVLEAVIAEGATTINIADTVGYGVPELYGNLVKTLRERIPNSHKAVFSV 201
                                                  ****************************************************************** PP

                                    TIGR00973 199 hchddlGlavanslaavkn.GarqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkei 263
                                                  hch+dlG+avansla v+  GarqvectinG+GeraGn++lee+vma+k+rkd++++e+g++t +i
  lcl|FitnessBrowser__Burk376:H281DRAFT_04556 202 HCHNDLGMAVANSLAGVQIgGARQVECTINGLGERAGNTSLEEIVMAVKTRKDYFGLELGLDTTQI 267
                                                  ******************637********************************************* PP

                                    TIGR00973 264 yrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknketyeilspesiGlkkeklvlgkrs 329
                                                    +s+lvs++tg +vq+nka+vG+nafah sGihqdGvlk + tyei+++e++G +++k+vlgk s
  lcl|FitnessBrowser__Burk376:H281DRAFT_04556 268 VPASKLVSQITGFVVQPNKAVVGANAFAHASGIHQDGVLKARDTYEIMRAEDVGWSANKIVLGKLS 333
                                                  ****************************************************************** PP

                                    TIGR00973 330 GraalkkrleelGfkld.eeeldklfekfkeladkkkevfdedlealvleelrq.eeeeklklekl 393
                                                  Gr+a+k+rl+elG+ ld e el+ +f +fkelad+k e+fded+ a+v+ee  + +++e++k+ +l
  lcl|FitnessBrowser__Burk376:H281DRAFT_04556 334 GRNAFKQRLQELGIALDsEAELNTAFARFKELADRKAEIFDEDIIAIVTEESAEaQQKEHYKFLSL 399
                                                  ***************972569****************************9988758999******* PP

                                    TIGR00973 394 qvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkdalg 459
                                                  + +s + + p a + ++++g+e +  a GnGpvda+++aie  ++   +ll ys++a ++g++a+g
  lcl|FitnessBrowser__Burk376:H281DRAFT_04556 400 SQHSETGEQPHAKIVFAMDGKEITGEARGNGPVDATLNAIETEVGSGSELLLYSVNAITTGTQAQG 465
                                                  ****************************************************************** PP

                                    TIGR00973 460 evkvvlelngkkysGrgvatdiveasakayvnaln 494
                                                  ev+v+l   g+ ++G+g + div asakay+ aln
  lcl|FitnessBrowser__Burk376:H281DRAFT_04556 466 EVTVRLSKSGRIVNGVGTDPDIVAASAKAYISALN 500
                                                  *********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (515 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: 00:00:00.01
# Mc/sec: 12.74
//
[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