Alignments for a candidate for leuA in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Bacteroides thetaiotaomicron VPI-5482

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate 351389 BT1861 2-isopropylmalate synthase (NCBI ptt file)

Query= reanno::Btheta:351389
         (498 letters)



>FitnessBrowser__Btheta:351389
          Length = 498

 Score =  979 bits (2530), Expect = 0.0
 Identities = 498/498 (100%), Positives = 498/498 (100%)

Query: 1   MDNRLFIFDTTLRDGEQVPGCQLNTVEKIQVAKALEALGVDVIEAGFPISSPGDFNSVIE 60
           MDNRLFIFDTTLRDGEQVPGCQLNTVEKIQVAKALEALGVDVIEAGFPISSPGDFNSVIE
Sbjct: 1   MDNRLFIFDTTLRDGEQVPGCQLNTVEKIQVAKALEALGVDVIEAGFPISSPGDFNSVIE 60

Query: 61  ISKAVTWPTICALTRAVQKDIDVAVDALKFAKHKRIHTGIGTSDSHIKYKFNSNREEIIE 120
           ISKAVTWPTICALTRAVQKDIDVAVDALKFAKHKRIHTGIGTSDSHIKYKFNSNREEIIE
Sbjct: 61  ISKAVTWPTICALTRAVQKDIDVAVDALKFAKHKRIHTGIGTSDSHIKYKFNSNREEIIE 120

Query: 121 RAVAAVKYARRFVDDVEFYAEDAGRTDNEYLARVVEAVIKAGATVVNIPDTTGYCLPSEY 180
           RAVAAVKYARRFVDDVEFYAEDAGRTDNEYLARVVEAVIKAGATVVNIPDTTGYCLPSEY
Sbjct: 121 RAVAAVKYARRFVDDVEFYAEDAGRTDNEYLARVVEAVIKAGATVVNIPDTTGYCLPSEY 180

Query: 181 GAKIKYLIDHVDGIDNAILSTHCHNDLGMATANTIAGVLNGARQVEVTINGIGERAGNTA 240
           GAKIKYLIDHVDGIDNAILSTHCHNDLGMATANTIAGVLNGARQVEVTINGIGERAGNTA
Sbjct: 181 GAKIKYLIDHVDGIDNAILSTHCHNDLGMATANTIAGVLNGARQVEVTINGIGERAGNTA 240

Query: 241 LEEIAMIIKSHHEIDIQTNINTQKIYPTSRMVSSLMNMPVQPNKAIVGRNAFAHSSGIHQ 300
           LEEIAMIIKSHHEIDIQTNINTQKIYPTSRMVSSLMNMPVQPNKAIVGRNAFAHSSGIHQ
Sbjct: 241 LEEIAMIIKSHHEIDIQTNINTQKIYPTSRMVSSLMNMPVQPNKAIVGRNAFAHSSGIHQ 300

Query: 301 DGVLKNVETYEIIDPHDVGIDDNSIVLTARSGRAALKNRLSLLGVNLDQEKLDKVYEEFL 360
           DGVLKNVETYEIIDPHDVGIDDNSIVLTARSGRAALKNRLSLLGVNLDQEKLDKVYEEFL
Sbjct: 301 DGVLKNVETYEIIDPHDVGIDDNSIVLTARSGRAALKNRLSLLGVNLDQEKLDKVYEEFL 360

Query: 361 KLADKKKDINDDDVLVLAGADRSQNHRIKLEYLQVTSGVGVRSVASLGLNISGEKFEACA 420
           KLADKKKDINDDDVLVLAGADRSQNHRIKLEYLQVTSGVGVRSVASLGLNISGEKFEACA
Sbjct: 361 KLADKKKDINDDDVLVLAGADRSQNHRIKLEYLQVTSGVGVRSVASLGLNISGEKFEACA 420

Query: 421 SGNGPVDAAIKALKKIVDRHMTLKEFTIQAISKGSDDVGKVHMQVEYDNQIYYGFGANTD 480
           SGNGPVDAAIKALKKIVDRHMTLKEFTIQAISKGSDDVGKVHMQVEYDNQIYYGFGANTD
Sbjct: 421 SGNGPVDAAIKALKKIVDRHMTLKEFTIQAISKGSDDVGKVHMQVEYDNQIYYGFGANTD 480

Query: 481 IIAASVEAYIDCINKFKA 498
           IIAASVEAYIDCINKFKA
Sbjct: 481 IIAASVEAYIDCINKFKA 498


Lambda     K      H
   0.317    0.134    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: 1020
Number of extensions: 21
Number of successful extensions: 1
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: 498
Length of database: 498
Length adjustment: 34
Effective length of query: 464
Effective length of database: 464
Effective search space:   215296
Effective search space used:   215296
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 351389 BT1861 (2-isopropylmalate synthase (NCBI ptt file))
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.2847208.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                      -----------
   1.4e-206  672.6  11.2   1.6e-206  672.5  11.2    1.0  1  FitnessBrowser__Btheta:351389  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Btheta:351389  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  672.5  11.2  1.6e-206  1.6e-206       1     494 []       4     494 ..       4     494 .. 0.98

  Alignments for each domain:
  == domain 1  score: 672.5 bits;  conditional E-value: 1.6e-206
                      TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravekdida 80 
                                    r+ ifdttlrdGeq pg +l++ ek+q+akale lgvd+ieaGfp+ss+gdf++v +i+++v  +++++l+rav+kdid+
  FitnessBrowser__Btheta:351389   4 RLFIFDTTLRDGEQVPGCQLNTVEKIQVAKALEALGVDVIEAGFPISSPGDFNSVIEISKAVTWPTICALTRAVQKDIDV 83 
                                    678***************************************************************************** PP

                      TIGR00973  81 aaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvveaaieaGa 160
                                    a++alk a++kriht i tsd h+++k+ ++++e++er+v+avkya+ fvddvef aedagrt+ e+larvvea+i+aGa
  FitnessBrowser__Btheta:351389  84 AVDALKFAKHKRIHTGIGTSDSHIKYKFNSNREEIIERAVAAVKYARRFVDDVEFYAEDAGRTDNEYLARVVEAVIKAGA 163
                                    ******************************************************************************** PP

                      TIGR00973 161 ttiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinGiGeraGnaalee 240
                                    t++niPdt Gy+lP+eyg+ ik+l ++v +id+ails hch+dlG+a+an++a v nGarqve+tinGiGeraGn+alee
  FitnessBrowser__Btheta:351389 164 TVVNIPDTTGYCLPSEYGAKIKYLIDHVDGIDNAILSTHCHNDLGMATANTIAGVLNGARQVEVTINGIGERAGNTALEE 243
                                    ******************************************************************************** PP

                      TIGR00973 241 vvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknketyeilspesiGlkk 320
                                    ++m++k  ++ ++++t+int++iy tsr+vs l +m+vq+nkaivG nafah+sGihqdGvlkn etyei++p ++G++ 
  FitnessBrowser__Btheta:351389 244 IAMIIKSHHE-IDIQTNINTQKIYPTSRMVSSLMNMPVQPNKAIVGRNAFAHSSGIHQDGVLKNVETYEIIDPHDVGIDD 322
                                    ******9876.69******************************************************************* PP

                      TIGR00973 321 eklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqvqsgee 400
                                    + +vl++rsGraalk+rl+ lG++ld+e+ldk++e+f++ladkkk++ d+d+  l+  +    +++++kle+lqv sg  
  FitnessBrowser__Btheta:351389 323 NSIVLTARSGRAALKNRLSLLGVNLDQEKLDKVYEEFLKLADKKKDINDDDVLVLAGADRS--QNHRIKLEYLQVTSGVG 400
                                    ***************************************************9877777666..56678************ PP

                      TIGR00973 401 svptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkysGrgvatd 480
                                      + a + l+++ge+ ea+a+GnGpvda +ka++ki++ ++ l+e++i+a ++g+d +g+v++++e++++ y G g++td
  FitnessBrowser__Btheta:351389 401 VRSVASLGLNISGEKFEACASGNGPVDAAIKALKKIVDRHMTLKEFTIQAISKGSDDVGKVHMQVEYDNQIYYGFGANTD 480
                                    ******************************************************************************** PP

                      TIGR00973 481 iveasakayvnaln 494
                                    i+ as++ay++ +n
  FitnessBrowser__Btheta:351389 481 IIAASVEAYIDCIN 494
                                    ************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (498 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 29.04
//
[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 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