Alignments for a candidate for leuC in Herbaspirillum autotrophicum IAM 14942

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Herbaspirillum autotrophicum IAM 14942

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_050463057.1 AKL27_RS11970 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_001189915.1:WP_050463057.1
          Length = 466

 Score =  589 bits (1518), Expect = e-173
 Identities = 290/466 (62%), Positives = 353/466 (75%), Gaps = 1/466 (0%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           M KTLY+KL+++HVV+  ++ T +LYIDRHL+HEVTSPQAF+GL+  GR   +       
Sbjct: 1   MLKTLYDKLWESHVVHTEQDGTAILYIDRHLLHEVTSPQAFEGLKLAGRQPWRNAANLMV 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
            DHNV T  +        +R+Q++ L  N KEF +  + +N   QGIVHV+GPEQG TLP
Sbjct: 61  ADHNVPTTNRANGIADPTSRLQVETLDANAKEFDLTYFGMNDKRQGIVHVIGPEQGATLP 120

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180
           GMT+VCGDSHT+THGAF  LA GIGTSEVEHVLATQTL   ++K++ ++V G    G+TA
Sbjct: 121 GMTVVCGDSHTSTHGAFACLAHGIGTSEVEHVLATQTLLAKKSKSLLVQVDGPLPHGVTA 180

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KDIVLA+IG+ G+AGGTG+ +EF G  IR LSMEGRMT+CNMAIE GA+AG++A D+TT 
Sbjct: 181 KDIVLAVIGRIGTAGGTGYAIEFAGSTIRSLSMEGRMTVCNMAIEAGARAGMIAVDDTTI 240

Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300
           NY+KGR  AP G  ++ AV+YW+TL TD GA FD VVTL A +I PQVTWGT+P  VI+V
Sbjct: 241 NYLKGRPFAPSGPHWERAVSYWRTLHTDPGAKFDLVVTLNAADIKPQVTWGTSPEMVIAV 300

Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360
           +  IPDP    D  +R   EKALAYM LKP   + ++ IDKVFIGSCTNSRIEDLR AA 
Sbjct: 301 DSRIPDPDKEKDATKRDGMEKALAYMALKPNTLIEDIRIDKVFIGSCTNSRIEDLREAAA 360

Query: 361 IAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419
           + +G+  A  V+ A+VVPGSG VK QAE EGLDKIF +AGFEWR PGCSMCLAMN DRL 
Sbjct: 361 VVRGKFRASNVKLAMVVPGSGLVKEQAEREGLDKIFKDAGFEWREPGCSMCLAMNADRLE 420

Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           PGERCASTSNRNFEGRQG GGRTHLVSPAMAAAA + GHF D+R++
Sbjct: 421 PGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAGIAGHFVDVRSL 466


Lambda     K      H
   0.317    0.134    0.396 

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: 724
Number of extensions: 27
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: 466
Length of database: 466
Length adjustment: 33
Effective length of query: 433
Effective length of database: 433
Effective search space:   187489
Effective search space used:   187489
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: 51 (24.3 bits)

Align candidate WP_050463057.1 AKL27_RS11970 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

# 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/TIGR00170.hmm
# target sequence database:        /tmp/gapView.108925.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 3-isopropylmalate dehydratase, large subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-240  784.5   0.1   1.7e-240  784.4   0.1    1.0  1  NCBI__GCF_001189915.1:WP_050463057.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001189915.1:WP_050463057.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  784.4   0.1  1.7e-240  1.7e-240       1     465 [.       1     465 [.       1     466 [] 1.00

  Alignments for each domain:
  == domain 1  score: 784.4 bits;  conditional E-value: 1.7e-240
                             TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve 73 
                                           m ktly+kl+++hvv+ ++++t +lyidrhl+hevtspqafegl+ agr+  r    l   dhn++t++r   
  NCBI__GCF_001189915.1:WP_050463057.1   1 MLKTLYDKLWESHVVHTEQDGTAILYIDRHLLHEVTSPQAFEGLKLAGRQPWRNAANLMVADHNVPTTNRANG 73 
                                           679********************************************************************** PP

                             TIGR00170  74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146
                                           i + +++lqv++l+ n+kef + +f++++++qgivhv+gpe+g tlpg+t+vcgdsht+thgaf +la gigt
  NCBI__GCF_001189915.1:WP_050463057.1  74 IADPTSRLQVETLDANAKEFDLTYFGMNDKRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAFACLAHGIGT 146
                                           ************************************************************************* PP

                             TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219
                                           sevehvlatqtl  +++k+l ++v+g l +g+takdi+la+ig+ig+aggtgy +efag +ir+lsme+rmtv
  NCBI__GCF_001189915.1:WP_050463057.1 147 SEVEHVLATQTLLAKKSKSLLVQVDGPLPHGVTAKDIVLAVIGRIGTAGGTGYAIEFAGSTIRSLSMEGRMTV 219
                                           ************************************************************************* PP

                             TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292
                                           cnmaieaga+ag+ia d+tt++y+k+r++ap g ++e av+yw+tl+td+gakfd vvtl+a di pqvtwgt
  NCBI__GCF_001189915.1:WP_050463057.1 220 CNMAIEAGARAGMIAVDDTTINYLKGRPFAPSGPHWERAVSYWRTLHTDPGAKFDLVVTLNAADIKPQVTWGT 292
                                           ************************************************************************* PP

                             TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365
                                           +p++v++v++ +pdp++  d  ++ ++ekalay+ l+p+t ++di++dkvfigsctnsriedlr+aa+vv+gk
  NCBI__GCF_001189915.1:WP_050463057.1 293 SPEMVIAVDSRIPDPDKEKDATKRDGMEKALAYMALKPNTLIEDIRIDKVFIGSCTNSRIEDLREAAAVVRGK 365
                                           ************************************************************************* PP

                             TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438
                                             a+nvkla+vvpgsglvk+qae+egldkif +agfewre+gcs+cl+mn d+l+++ercastsnrnfegrqg
  NCBI__GCF_001189915.1:WP_050463057.1 366 FRASNVKLAMVVPGSGLVKEQAEREGLDKIFKDAGFEWREPGCSMCLAMNADRLEPGERCASTSNRNFEGRQG 438
                                           ************************************************************************* PP

                             TIGR00170 439 kgarthlvspamaaaaavagkfvdire 465
                                           +g+rthlvspamaaaa++ag+fvd+r 
  NCBI__GCF_001189915.1:WP_050463057.1 439 AGGRTHLVSPAMAAAAGIAGHFVDVRS 465
                                           *************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (466 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.44
//
[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