Alignments for a candidate for leuA in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Thiomicrospira cyclica ALM1

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_013834785.1 THICY_RS01160 2-isopropylmalate synthase

Query= BRENDA::Q9JZG1
         (517 letters)



>NCBI__GCF_000214825.1:WP_013834785.1
          Length = 516

 Score =  647 bits (1668), Expect = 0.0
 Identities = 322/514 (62%), Positives = 408/514 (79%), Gaps = 1/514 (0%)

Query: 5   NRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAIA 64
           + +IIFDTTLRDGEQSPGA+MTKEEK+R+A+QLEK+ VD+IEAGF AAS GDFE+V A+A
Sbjct: 3   DHLIIFDTTLRDGEQSPGASMTKEEKVRIAKQLEKMRVDVIEAGFPAASDGDFESVQAVA 62

Query: 65  KTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEAA 124
           K I  STVC L+RA+E DI +AG+A+APA   RIHTFIATSPIHME KL+M P QV+E A
Sbjct: 63  KVIKDSTVCGLARAVEHDIVKAGQAIAPANSGRIHTFIATSPIHMEMKLRMTPDQVVERA 122

Query: 125 VKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTEE 184
           V AVK AR++TD+VEFS EDA RSE+DFL  +  A I+AGATTINIPDTVGY++P +   
Sbjct: 123 VWAVKRARDFTDNVEFSPEDAGRSELDFLCRVIEAAIDAGATTINIPDTVGYNVPDQFGY 182

Query: 185 FFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNASVE 244
            F++L+ + PN  K ++SAHCHNDLGLAVANS+AA+  GARQVECT+NGLGERAGN ++E
Sbjct: 183 LFKQLLERIPNADKAIFSAHCHNDLGLAVANSIAAVTNGARQVECTINGLGERAGNTALE 242

Query: 245 EIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIHQD 304
           E+VMA++ R D F ++T I T +I+ +S+LVS ITG+ VQPNKAIVGANAF+HESGIHQD
Sbjct: 243 ELVMAVRTRQDYFSVDTRIHTPEILTASRLVSNITGFSVQPNKAIVGANAFAHESGIHQD 302

Query: 305 GVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFARFK 364
           GVLKHRETYEIM AE VGW+TN++ LGK SGRNAFKT+L +LG+E E+E+ LN  F RFK
Sbjct: 303 GVLKHRETYEIMRAEDVGWSTNKMVLGKHSGRNAFKTRLQELGVEFETEQQLNDTFVRFK 362

Query: 365 ELADKKREIFDEDLHALVSD-EMGSMNAESYKFISQKISTETGEEPRADIVFSIKGEEKR 423
           ELAD+K EI+DEDL ALV++  +  +  ES + ++ K++ E GE+P A I  S+ G+E  
Sbjct: 363 ELADRKHEIYDEDLQALVTEANIERVENESIRLVALKVAAEMGEQPSATITLSVDGQEFT 422

Query: 424 ASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQGA 483
           ASA G G VDA FKAIE +  S   L++YSV+ VT GT+S GETSVRL +G R+VNGQG+
Sbjct: 423 ASAMGGGVVDATFKAIEQILNSKTTLELYSVSNVTNGTDSLGETSVRLEKGGRIVNGQGS 482

Query: 484 DTDVLVATAKAYLSALSKLEFSAAKPKAQGSGTI 517
           DTD++ A+AKAY++AL+K   +A K   Q   T+
Sbjct: 483 DTDIVTASAKAYINALNKFSDAAIKAHPQRQETV 516


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: 698
Number of extensions: 28
Number of successful extensions: 2
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: 516
Length adjustment: 35
Effective length of query: 482
Effective length of database: 481
Effective search space:   231842
Effective search space used:   231842
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_013834785.1 THICY_RS01160 (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.25942.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-224  731.8   7.7   1.9e-224  731.6   7.7    1.0  1  lcl|NCBI__GCF_000214825.1:WP_013834785.1  THICY_RS01160 2-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214825.1:WP_013834785.1  THICY_RS01160 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  731.6   7.7  1.9e-224  1.9e-224       2     494 .]       5     499 ..       4     499 .. 0.98

  Alignments for each domain:
  == domain 1  score: 731.6 bits;  conditional E-value: 1.9e-224
                                 TIGR00973   2 vlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvgl 70 
                                               ++ifdttlrdGeq+pgas+t eek++iak+le++ vd+ieaGfp++s gdfe+vq +a+ +k+++v+gl
  lcl|NCBI__GCF_000214825.1:WP_013834785.1   5 LIIFDTTLRDGEQSPGASMTKEEKVRIAKQLEKMRVDVIEAGFPAASDGDFESVQAVAKVIKDSTVCGL 73 
                                               68******************************************************************* PP

                                 TIGR00973  71 aravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaed 139
                                               arave+di  a +a+ pa+  rihtfiats+ih+e+kl++t d+v+er+v avk+a++f+d+vefs+ed
  lcl|NCBI__GCF_000214825.1:WP_013834785.1  74 ARAVEHDIVKAGQAIAPANSGRIHTFIATSPIHMEMKLRMTPDQVVERAVWAVKRARDFTDNVEFSPED 142
                                               ********************************************************************* PP

                                 TIGR00973 140 agrteleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlav 208
                                               agr+el+fl+rv+eaai+aGattiniPdtvGy +P+++g l+k+l e++Pn dkai+s+hch+dlGlav
  lcl|NCBI__GCF_000214825.1:WP_013834785.1 143 AGRSELDFLCRVIEAAIDAGATTINIPDTVGYNVPDQFGYLFKQLLERIPNADKAIFSAHCHNDLGLAV 211
                                               ********************************************************************* PP

                                 TIGR00973 209 anslaavknGarqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgml 277
                                               ans+aav nGarqvectinG+GeraGn+alee+vma+++r+d+++v+t i+t ei  +srlvs++tg  
  lcl|NCBI__GCF_000214825.1:WP_013834785.1 212 ANSIAAVTNGARQVECTINGLGERAGNTALEELVMAVRTRQDYFSVDTRIHTPEILTASRLVSNITGFS 280
                                               ********************************************************************* PP

                                 TIGR00973 278 vqrnkaivGdnafahesGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkld 346
                                               vq+nkaivG+nafahesGihqdGvlk++etyei+++e++G +++k+vlgk+sGr+a+k+rl+elG++++
  lcl|NCBI__GCF_000214825.1:WP_013834785.1 281 VQPNKAIVGANAFAHESGIHQDGVLKHRETYEIMRAEDVGWSTNKMVLGKHSGRNAFKTRLQELGVEFE 349
                                               *******************************************************************86 PP

                                 TIGR00973 347 .eeeldklfekfkeladkkkevfdedlealvlee.lrqeeeeklkleklqvqsgeesvptatvklkvkg 413
                                                e++l+  f +fkelad+k+e++dedl+alv+e  +++ e+e+++l+ l+v +   + p at++l v+g
  lcl|NCBI__GCF_000214825.1:WP_013834785.1 350 tEQQLNDTFVRFKELADRKHEIYDEDLQALVTEAnIERVENESIRLVALKVAAEMGEQPSATITLSVDG 418
                                               2678***************************986155678899************************** PP

                                 TIGR00973 414 eekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkysGrgvatdiv 482
                                               +e +a+a+G G vda++kaie+il+ ++ l+ ys+  +++g+d+lge +v+le  g+ ++G+g +tdiv
  lcl|NCBI__GCF_000214825.1:WP_013834785.1 419 QEFTASAMGGGVVDATFKAIEQILNSKTTLELYSVSNVTNGTDSLGETSVRLEKGGRIVNGQGSDTDIV 487
                                               ********************************************************************* PP

                                 TIGR00973 483 easakayvnaln 494
                                                asakay+naln
  lcl|NCBI__GCF_000214825.1:WP_013834785.1 488 TASAKAYINALN 499
                                               ***********9 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.72
//
[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