Alignments for a candidate for leuA in Desulfarculus baarsii DSM 2075

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Desulfarculus baarsii DSM 2075

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_013257580.1 DEBA_RS03775 2-isopropylmalate synthase

Query= BRENDA::K4C627
         (612 letters)



>NCBI__GCF_000143965.1:WP_013257580.1
          Length = 516

 Score =  484 bits (1245), Expect = e-141
 Identities = 260/525 (49%), Positives = 361/525 (68%), Gaps = 28/525 (5%)

Query: 69  NYVRIFDTTLRDGEQSPGATMTTKEKLDVARQLAKLGVDIIEAGFPASSEADLEAVKLIA 128
           NYV+IFDTTLRDGEQSPGA+M  +EKL +AR+LAKLGVDIIEAGFPA+S  D EAV+LIA
Sbjct: 3   NYVKIFDTTLRDGEQSPGASMNKEEKLRLARKLAKLGVDIIEAGFPAASPGDFEAVRLIA 62

Query: 129 KEVGNGVYEEGYVPVICGLARCNKKDIDKAWEAVKYAKKPRIHTFIATSEIHMNYKLKMS 188
            ++  G       PV+CGL+R    DI++ W+AV+ A+KPRIH F+ATS+IH+ YKL+M+
Sbjct: 63  GDLRGG-------PVVCGLSRTRPADIERCWQAVREAEKPRIHVFLATSDIHLQYKLQMT 115

Query: 189 RDQVVEKARSMVAYARSIGCEDVEFSPEDAGRSDPEFLYHILGEVIKAGATTLNIPDTVG 248
           R QV+++ RS V +AR + CEDV++S EDA RSDP+FL   +   ++AGATT+NIPDTVG
Sbjct: 116 RQQVLDEIRSGVGHARGL-CEDVQWSAEDASRSDPDFLCQCVRVALEAGATTINIPDTVG 174

Query: 249 YTVPEEFGQLIAKIKANTPGVEDVIISTHCQNDLGLSTANTLAGACAGARQLEVTINGIG 308
           Y +P EF + I+ I+AN P V    +S HC +DLG + AN++AG  AGARQ+E  INGIG
Sbjct: 175 YALPHEFYERISYIRANVPEVARATLSVHCHDDLGHAVANSIAGVRAGARQVEGCINGIG 234

Query: 309 ERAGNASLEEVVMALKCRGEQVLGGLYTGINTQHILMSSKMVEEYSGLHVQPHKAIVGAN 368
           ERAGNA+LEEV+M L  R +++  GL TG+N   I  +S++V   SGL VQP+KAIVGAN
Sbjct: 235 ERAGNAALEEVIMTLATRQKEL--GLITGVNKAEIHSTSRLVTMISGLPVQPNKAIVGAN 292

Query: 369 AFAHESGIHQDGMLKHKDTYEIISPEDIGLNRANESGIVLGKLSGRHALQAKMLELGYEI 428
           AFAHESGIH DG+LK   TYEI++PE++GL     + +VLGK SGR AL+  +   GYE+
Sbjct: 293 AFAHESGIHVDGVLKQPLTYEIMTPEEVGL---ASNTVVLGKHSGRAALRNWLSGNGYEL 349

Query: 429 EGKELDDLFWRFKSVAEKKKKITDDDLVALMSDEVFQPQFVWQLQNVQVTSGSLGLSTAT 488
           + ++ + LF  FK +A+KKK+I +DDL AL++DE+ +    W+L  + V +G+     AT
Sbjct: 350 DRQQCESLFEAFKRLADKKKEIENDDLEALIADEILRIPLRWKLDYLNVMAGTEVEPVAT 409

Query: 489 VKLIDADGREHISCSVGTGPVDAAYKAVDLIVKVPVTLLEYSMNAVTQGIDAIASTRVLI 548
           V++ D D       + G GPVDA Y A+  I      L+ Y + ++T G+DA     V +
Sbjct: 410 VRVFDGDSLRR-EAAFGVGPVDAVYNAIRKITGTQAKLMRYGVASITGGVDAQGEVTVKL 468

Query: 549 RGENGHTSTHAVTGETIHRTFSGTGADMDIVISSVRAYVGALNKM 593
           + ENG+ +              G GAD DI+++S +A++  +N++
Sbjct: 469 Q-ENGNEAL-------------GKGADSDILVASAKAFLNGINRL 499


Lambda     K      H
   0.316    0.132    0.377 

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: 777
Number of extensions: 30
Number of successful extensions: 7
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: 612
Length of database: 516
Length adjustment: 36
Effective length of query: 576
Effective length of database: 480
Effective search space:   276480
Effective search space used:   276480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate WP_013257580.1 DEBA_RS03775 (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.2805274.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-205  668.1   0.0   3.9e-205  667.9   0.0    1.0  1  NCBI__GCF_000143965.1:WP_013257580.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000143965.1:WP_013257580.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  667.9   0.0  3.9e-205  3.9e-205       2     494 .]       5     497 ..       4     497 .. 0.98

  Alignments for each domain:
  == domain 1  score: 667.9 bits;  conditional E-value: 3.9e-205
                             TIGR00973   2 vlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevkn.arvvglara 73 
                                           v+ifdttlrdGeq+pgas++ eekl++a++l++lgvdiieaGfp++s+gdfeav+ ia +++  ++v+gl+r+
  NCBI__GCF_000143965.1:WP_013257580.1   5 VKIFDTTLRDGEQSPGASMNKEEKLRLARKLAKLGVDIIEAGFPAASPGDFEAVRLIAGDLRGgPVVCGLSRT 77 
                                           89**********************************************************985278******* PP

                             TIGR00973  74 vekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrtele 146
                                              di+  ++a+++aek rih+f+atsdihl++kl++t+++vl+ i++ v +a+ + +dv++saeda+r++ +
  NCBI__GCF_000143965.1:WP_013257580.1  78 RPADIERCWQAVREAEKPRIHVFLATSDIHLQYKLQMTRQQVLDEIRSGVGHARGLCEDVQWSAEDASRSDPD 150
                                           ************************************************************************* PP

                             TIGR00973 147 flarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGa 219
                                           fl++ v+ a+eaGattiniPdtvGyalP+e+ e i++++ nvP++ +a+lsvhchddlG avans+a v++Ga
  NCBI__GCF_000143965.1:WP_013257580.1 151 FLCQCVRVALEAGATTINIPDTVGYALPHEFYERISYIRANVPEVARATLSVHCHDDLGHAVANSIAGVRAGA 223
                                           ************************************************************************* PP

                             TIGR00973 220 rqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafah 292
                                           rqve++inGiGeraGnaaleev+m l +r+  l++ tg+n+ ei+ tsrlv+ ++g++vq+nkaivG+nafah
  NCBI__GCF_000143965.1:WP_013257580.1 224 RQVEGCINGIGERAGNAALEEVIMTLATRQKELGLITGVNKAEIHSTSRLVTMISGLPVQPNKAIVGANAFAH 296
                                           ************************************************************************* PP

                             TIGR00973 293 esGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkk 365
                                           esGih dGvlk+  tyei++pe++Gl ++++vlgk+sGraal++ l+  G++ld ++ + lfe+fk+ladkkk
  NCBI__GCF_000143965.1:WP_013257580.1 297 ESGIHVDGVLKQPLTYEIMTPEEVGLASNTVVLGKHSGRAALRNWLSGNGYELDRQQCESLFEAFKRLADKKK 369
                                           ************************************************************************* PP

                             TIGR00973 366 evfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekile 438
                                           e+ ++dleal+ +e+ + +  ++kl++l+v +g+e  p atv++   ++ +++aa G Gpvdavy+ai ki++
  NCBI__GCF_000143965.1:WP_013257580.1 370 EIENDDLEALIADEILRIP-LRWKLDYLNVMAGTEVEPVATVRVFDGDSLRREAAFGVGPVDAVYNAIRKITG 441
                                           ***************9655.56*********************9775666*********************** PP

                             TIGR00973 439 levklleysitakgegkdalgevkvvlelngkkysGrgvatdiveasakayvnaln 494
                                           ++ kl+ y + + + g da+gev+v+l+ ng+++ G+g++ di+ asaka++n +n
  NCBI__GCF_000143965.1:WP_013257580.1 442 TQAKLMRYGVASITGGVDAQGEVTVKLQENGNEALGKGADSDILVASAKAFLNGIN 497
                                           *****************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (516 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: 00:00:00.00
# Mc/sec: 35.25
//
[ok]

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