Alignments for a candidate for leuA in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Kyrpidia tusciae DSM 2912

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_013074979.1 BTUS_RS04780 2-isopropylmalate synthase

Query= BRENDA::Q72JC9
         (520 letters)



>NCBI__GCF_000092905.1:WP_013074979.1
          Length = 516

 Score =  509 bits (1311), Expect = e-149
 Identities = 269/503 (53%), Positives = 357/503 (70%), Gaps = 3/503 (0%)

Query: 5   RHIRIFDTTLRDGEQSPGVALSLDQKLEIAQALAQLNVDIIEAGFPVSGPMEFEAVRRIA 64
           R I +FDTTLRDGEQSPG+ LS ++KLEIA+ L +L VD+IEAGF  + P +FE+V  IA
Sbjct: 2   RTIEVFDTTLRDGEQSPGINLSREEKLEIARQLGRLGVDVIEAGFAAASPGDFESVAEIA 61

Query: 65  TEVKGPIIAALARTHTLDIDQAAKALEKAEKPRIHVFTSASKVHLQYMLRKTEEEVLEMA 124
            EV+G  + +LAR+   DID+A +AL  AE PRIHVF + S +HLQ+ LR T E+VLE  
Sbjct: 62  REVRGLTVCSLARSVQSDIDRAYEALRDAEDPRIHVFLATSDIHLQHKLRLTREQVLEQI 121

Query: 125 DRMVRYARRYVDDVEFSAQDVMRADWEFVKRLYEVAIEAGATTINIPDTTGYGTPQEYGA 184
           D  VRYA +Y+ +VEFSA+D  R D +F+ ++ EVAI AGA   N+PDT GY TPQEY  
Sbjct: 122 DAAVRYAVKYMSNVEFSAEDAGRTDIDFLCQVAEVAIRAGAKVFNVPDTVGYLTPQEYAG 181

Query: 185 LIRRIRDEVVRGRDVIISTHTHDDLGMATANALAGVENGAGQIECTINGIGERAGNCALE 244
            IR +R+ V     + +S+H HDDLGMA +N LAG+E G  Q+E TINGIGERAGN +LE
Sbjct: 182 KIRALRERVPGIAKIKLSSHCHDDLGMAVSNTLAGIEAGITQVEVTINGIGERAGNASLE 241

Query: 245 EVVMALYVRRDWYKAYTRINTREIYRVSRLVERYTGMPVPPNKAIVGDNAFAHESGIHQD 304
           EVVMAL  R D+Y+A T I   +IYR SRLV + TG  VPPNKAIVG NAFAHESGIHQD
Sbjct: 242 EVVMALATRPDFYQAKTNIVLNQIYRTSRLVSKLTGFVVPPNKAIVGANAFAHESGIHQD 301

Query: 305 GVIKHRATYEIMDAELIGRRPAVLVLGKHSGRAAFKKALEDLGYKDLSEEEVKKLFARFK 364
           GV+K + TYEIM  E IG   + LVLGKHSGR AF++ L ++GY+ LS+EEV +LF RFK
Sbjct: 302 GVLKEKLTYEIMKPETIGVAESKLVLGKHSGRHAFREKLTEMGYQ-LSDEEVNELFKRFK 360

Query: 365 EIAEKKGPLSAEELQALV-ESEREPTSHFFQLEHVQFFSGSGLLPTATVKVKTPDGERV- 422
           ++ +KK  ++ +++ ALV +S     S  +QLE++   +G+  +PTAT++V+  DG  V 
Sbjct: 361 DLCDKKKTVTDDDIAALVDDSHTVERSDLYQLEYLHISAGNTAVPTATLRVRLADGTVVE 420

Query: 423 ATHTGDGPVDAVYKAIQEAIGLRPELELYRVEAITGSTEALGQVTVRLRLGELQAVGVGV 482
               G+G VDA+Y+AI    G   EL  Y+++++TG  +ALG+V V++R GE    G GV
Sbjct: 421 EAAVGNGAVDAIYQAIDRVTGGATELVSYQIQSVTGGRDALGEVRVQVRQGEAVVSGRGV 480

Query: 483 SPDIIEASALAFLDAAGKLASGR 505
           S D++EASA A+LDA  +LA+G+
Sbjct: 481 STDVLEASAKAYLDAVNRLAAGQ 503


Lambda     K      H
   0.318    0.134    0.378 

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: 650
Number of extensions: 23
Number of successful extensions: 4
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: 520
Length of database: 516
Length adjustment: 35
Effective length of query: 485
Effective length of database: 481
Effective search space:   233285
Effective search space used:   233285
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_013074979.1 BTUS_RS04780 (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.25809.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-226  739.1   6.6   1.2e-226  738.9   6.6    1.0  1  lcl|NCBI__GCF_000092905.1:WP_013074979.1  BTUS_RS04780 2-isopropylmalate s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013074979.1  BTUS_RS04780 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  738.9   6.6  1.2e-226  1.2e-226       2     494 .]       4     497 ..       3     497 .. 0.99

  Alignments for each domain:
  == domain 1  score: 738.9 bits;  conditional E-value: 1.2e-226
                                 TIGR00973   2 vlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvgl 70 
                                               + +fdttlrdGeq+pg++l+ eekl+ia++l rlgvd+ieaGf+++s+gdfe+v +iarev+  +v++l
  lcl|NCBI__GCF_000092905.1:WP_013074979.1   4 IEVFDTTLRDGEQSPGINLSREEKLEIARQLGRLGVDVIEAGFAAASPGDFESVAEIAREVRGLTVCSL 72 
                                               789****************************************************************** PP

                                 TIGR00973  71 aravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaed 139
                                               ar+v++did a+eal++ae  rih+f+atsdihl++kl+ t+++vle+i +av+ya +++ +vefsaed
  lcl|NCBI__GCF_000092905.1:WP_013074979.1  73 ARSVQSDIDRAYEALRDAEDPRIHVFLATSDIHLQHKLRLTREQVLEQIDAAVRYAVKYMSNVEFSAED 141
                                               ********************************************************************* PP

                                 TIGR00973 140 agrteleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlav 208
                                               agrt+++fl++v e ai aGa + n+PdtvGy++P+ey+  i+ l+e+vP+i k++ls hchddlG+av
  lcl|NCBI__GCF_000092905.1:WP_013074979.1 142 AGRTDIDFLCQVAEVAIRAGAKVFNVPDTVGYLTPQEYAGKIRALRERVPGIAKIKLSSHCHDDLGMAV 210
                                               ********************************************************************* PP

                                 TIGR00973 209 anslaavknGarqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgml 277
                                               +n+la +++G +qve+tinGiGeraGna+leevvmal +r df++ +t+i  ++iyrtsrlvskltg +
  lcl|NCBI__GCF_000092905.1:WP_013074979.1 211 SNTLAGIEAGITQVEVTINGIGERAGNASLEEVVMALATRPDFYQAKTNIVLNQIYRTSRLVSKLTGFV 279
                                               ********************************************************************* PP

                                 TIGR00973 278 vqrnkaivGdnafahesGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkld 346
                                               v++nkaivG+nafahesGihqdGvlk+k tyei++pe+iG+ ++klvlgk+sGr+a++++l+e+G++l+
  lcl|NCBI__GCF_000092905.1:WP_013074979.1 280 VPPNKAIVGANAFAHESGIHQDGVLKEKLTYEIMKPETIGVAESKLVLGKHSGRHAFREKLTEMGYQLS 348
                                               ********************************************************************* PP

                                 TIGR00973 347 eeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvk.ge 414
                                               +ee+++lf++fk+l+dkkk v+d+d+ alv ++ + e+++ ++le+l++++g++ vptat+++++  g 
  lcl|NCBI__GCF_000092905.1:WP_013074979.1 349 DEEVNELFKRFKDLCDKKKTVTDDDIAALVDDSHTVERSDLYQLEYLHISAGNTAVPTATLRVRLAdGT 417
                                               ****************************************************************99566 PP

                                 TIGR00973 415 ekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkysGrgvatdive 483
                                                 e+aa GnG+vda+y+ai+++++  ++l+ y+i++++ g+dalgev+v+++  +  +sGrgv+td++e
  lcl|NCBI__GCF_000092905.1:WP_013074979.1 418 VVEEAAVGNGAVDAIYQAIDRVTGGATELVSYQIQSVTGGRDALGEVRVQVRQGEAVVSGRGVSTDVLE 486
                                               6******************************************************************** PP

                                 TIGR00973 484 asakayvnaln 494
                                               asakay++a+n
  lcl|NCBI__GCF_000092905.1:WP_013074979.1 487 ASAKAYLDAVN 497
                                               **********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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.62
//
[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