Alignments for a candidate for leuA in Allochromatium vinosum DSM 180

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Allochromatium vinosum DSM 180

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate WP_012970588.1 ALVIN_RS06805 2-isopropylmalate synthase

Query= SwissProt::P42455
         (616 letters)



>NCBI__GCF_000025485.1:WP_012970588.1
          Length = 547

 Score =  527 bits (1357), Expect = e-154
 Identities = 276/564 (48%), Positives = 379/564 (67%), Gaps = 26/564 (4%)

Query: 40  RYMPFEVEVEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFELLVQ 99
           RY P  V    ++LP+R WP++ I  AP W +VDLRDGNQAL +PM+ E+KRR+++LLV+
Sbjct: 8   RYRPGPV----VNLPNRQWPNRTIREAPIWASVDLRDGNQALHEPMNVEQKRRLWDLLVR 63

Query: 100 MGFKEIEVGFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGAKNV 159
           +GFKEIEVGFP+ASQ D+DFVR +IE+  IP+DVTIQVLVQARE LIRRT+EA  G +  
Sbjct: 64  LGFKEIEVGFPAASQPDYDFVRWLIEEDRIPEDVTIQVLVQAREDLIRRTYEALAGVRQA 123

Query: 160 IVHFYNSTSILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFTGTE 219
           IVH YNSTS +QR+ VF  D+  VK +A   AE +   A+DYP+T W +QYSPES+T TE
Sbjct: 124 IVHVYNSTSPVQRDWVFGQDREGVKAIARQGAEWVAQGARDYPETRWTFQYSPESYTATE 183

Query: 220 VEYAKEVVDAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSIILSL 279
            +YA EV +AV++V  PTPE P IINLP+TVE+ +PNV+AD +E    +++RRD+I+LS+
Sbjct: 184 PDYAIEVCEAVLDVWQPTPERPCIINLPATVEVSSPNVFADQVEHFANHISRRDAIVLSV 243

Query: 280 HPHNDRGTGVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLDFTD 339
           H HNDRG  V AAEL  +AGADR+EG L GNGERTGN  L+TLA+N+ +QG+DP+LD + 
Sbjct: 244 HTHNDRGGAVAAAELALLAGADRVEGTLLGNGERTGNADLLTLAMNLYSQGIDPKLDLSR 303

Query: 340 IRQIRSTVEYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASSTEVS 399
             +I +    C  L V  RHP+ G+LV+ A+SGSHQDA+ K L                 
Sbjct: 304 PDEIVAVCTECTGLPVHPRHPWVGELVYMAYSGSHQDAIRKCLS---------------- 347

Query: 400 WEQLRDTEWEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQVEF 459
             Q  D  W V YLPIDP D+GR+Y+AVIRVNSQSGKGGVA++++ + GL +PR +QVE 
Sbjct: 348 -RQTPDAPWNVAYLPIDPADLGRNYQAVIRVNSQSGKGGVAFVLEQEFGLSLPRWLQVEL 406

Query: 460 STVVQNVTDAEGGEVNSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAELIH 519
           + +VQ  ++  GG +++  +  IF   ++   AP   +  R++     N    I A +  
Sbjct: 407 AALVQRESETRGGVLDAAQIRAIFERHFIVDQAPHRLLGYRLD----RNGHDVIEARIGT 462

Query: 520 NGKDVTVDGRGNGPLAAYANALEK-LGIDVEIQEYNQHARTSGDDAEAAAYVLAEVNGRK 578
              +  + G+G G +AA+ +A  +  G  + + +Y +HA   G DAEAAAYV  E++G+ 
Sbjct: 463 PDGERMLHGQGQGAMAAFVDAWTRWSGRSLSVLDYQEHAIGEGTDAEAAAYVRVEIDGQA 522

Query: 579 VWGVGIAGSITYASLKAVTSAVNR 602
           + G  I      ASL+A+ SA+NR
Sbjct: 523 ITGAAIDRDTVAASLRALLSALNR 546


Lambda     K      H
   0.316    0.133    0.390 

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: 971
Number of extensions: 34
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: 616
Length of database: 547
Length adjustment: 36
Effective length of query: 580
Effective length of database: 511
Effective search space:   296380
Effective search space used:   296380
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_012970588.1 ALVIN_RS06805 (2-isopropylmalate synthase)
to HMM TIGR00970 (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/TIGR00970.hmm
# target sequence database:        /tmp/gapView.15818.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00970  [M=564]
Accession:   TIGR00970
Description: leuA_yeast: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.8e-216  704.5   0.0   5.5e-216  704.4   0.0    1.0  1  lcl|NCBI__GCF_000025485.1:WP_012970588.1  ALVIN_RS06805 2-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025485.1:WP_012970588.1  ALVIN_RS06805 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  704.4   0.0  5.5e-216  5.5e-216       3     561 ..       7     546 ..       5     547 .] 0.97

  Alignments for each domain:
  == domain 1  score: 704.4 bits;  conditional E-value: 5.5e-216
                                 TIGR00970   3 kkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfps 71 
                                               ++y+p   ++l+nr+wp++ i  ap w svdlrdGnqal +pm+ve+k+r+++llvr+Gfkeievgfp+
  lcl|NCBI__GCF_000025485.1:WP_012970588.1   7 RRYRPGPVVNLPNRQWPNRTIREAPIWASVDLRDGNQALHEPMNVEQKRRLWDLLVRLGFKEIEVGFPA 75 
                                               69******************************************************************* PP

                                 TIGR00970  72 asqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasr 140
                                               asq d+dfvr +ie+  ip+dvtiqvl+q+re+li+rt eal+G ++aivh+yn+ts+++r+ vf ++r
  lcl|NCBI__GCF_000025485.1:WP_012970588.1  76 ASQPDYDFVRWLIEEDRIPEDVTIQVLVQAREDLIRRTYEALAGVRQAIVHVYNSTSPVQRDWVFGQDR 144
                                               ********************************************************************* PP

                                 TIGR00970 141 eevlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnl 209
                                               e v a+a +g   +  +++ a +++etrw+f+yspes++ te+++a+evceav +v++pt+erp i nl
  lcl|NCBI__GCF_000025485.1:WP_012970588.1 145 EGVKAIARQG---AEWVAQGARDYPETRWTFQYSPESYTATEPDYAIEVCEAVLDVWQPTPERPCIINL 210
                                               **********...6667788999********************************************** PP

                                 TIGR00970 210 patvevatpnvyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertG 278
                                               patvev++pnv+ad++e+++++i+ r+ ++ls+h+hndrG avaaael llaGadr+eG l+GnGertG
  lcl|NCBI__GCF_000025485.1:WP_012970588.1 211 PATVEVSSPNVFADQVEHFANHISRRDAIVLSVHTHNDRGGAVAAAELALLAGADRVEGTLLGNGERTG 279
                                               ********************************************************************* PP

                                 TIGR00970 279 nvdlvtlalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGlda 347
                                               n dl+tla+nly+qG++p+ld+s  dei+ v  +c  +pvh+rhp+ G+lv+ a+sGshqdai+k l  
  lcl|NCBI__GCF_000025485.1:WP_012970588.1 280 NADLLTLAMNLYSQGIDPKLDLSRPDEIVAVCTECTGLPVHPRHPWVGELVYMAYSGSHQDAIRKCLSR 348
                                               ******************************************************************975 PP

                                 TIGR00970 348 ldkkkaaadtlwkvpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvkd 416
                                               +     + d+ w+v ylp+dp d+gr+y+avirvnsqsGkGGva+vl ++ Gl+lpr lq+e++ +v+ 
  lcl|NCBI__GCF_000025485.1:WP_012970588.1 349 Q-----TPDAPWNVAYLPIDPADLGRNYQAVIRVNSQSGKGGVAFVLEQEFGLSLPRWLQVELAALVQR 412
                                               4.....45789********************************************************** PP

                                 TIGR00970 417 iadskGkelsskeisdlfkeeyllnveqlerislvdyaveddGteskvitavvkikgekkdieGsGnGp 485
                                                ++++G+ l++ +i  +f+ ++ + ++ ++  +l  y ++ +G  + vi+a +   + ++ ++G G+G 
  lcl|NCBI__GCF_000025485.1:WP_012970588.1 413 ESETRGGVLDAAQIRAIFERHFIV-DQAPH--RLLGYRLDRNG--HDVIEARIGTPDGERMLHGQGQGA 476
                                               *******************99999.55555..56789******..89********************** PP

                                 TIGR00970 486 lsalvdaladllnvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvGiaedvtsaslra 554
                                               ++a+vda ++    +++v+dy+eha+g G da+aa+yv++ +  ++      + G  i+ d  +aslra
  lcl|NCBI__GCF_000025485.1:WP_012970588.1 477 MAAFVDAWTRWSGRSLSVLDYQEHAIGEGTDAEAAAYVRVEIDGQA------ITGAAIDRDTVAASLRA 539
                                               ***************************************9998888......89*************** PP

                                 TIGR00970 555 vlsavnr 561
                                               +lsa+nr
  lcl|NCBI__GCF_000025485.1:WP_012970588.1 540 LLSALNR 546
                                               *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (547 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 9.82
//
[ok]

This GapMind analysis is from Apr 10 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