Alignments for a candidate for leuC in Thermus aquaticus YT-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Thermus aquaticus YT-1

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_053767879.1 BVI061214_RS07580 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_001280255.1:WP_053767879.1
          Length = 470

 Score =  484 bits (1247), Expect = e-141
 Identities = 251/466 (53%), Positives = 320/466 (68%), Gaps = 2/466 (0%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           M KTLY+K+++AH V +  N    L+ID HL+HEVTSPQAF  L+  G  VR P +TFAT
Sbjct: 1   MGKTLYDKVWEAHEVRKLRNGQSQLFIDLHLLHEVTSPQAFGMLKDLGLKVRYPHRTFAT 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
           +DH V T  +       +A+  ++ L +N KE G+  +DL    QGIVHV+GP+ G+T P
Sbjct: 61  VDHIVPTHDRTEPFQDPLAQNMLEALRRNTKEHGITFFDLGSGNQGIVHVIGPQLGLTQP 120

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180
           GMTI CGDSHT+THGAFGA+AFGIGTS+V  VLATQ+L   + K  +I V GK  PG+ A
Sbjct: 121 GMTIACGDSHTSTHGAFGAVAFGIGTSQVRDVLATQSLAAKKLKVRRINVDGKLGPGVYA 180

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KD++L II   G  GG G+  E+ G  +  + ME RMTLCNM+IE GA+ G V PDETTF
Sbjct: 181 KDVILHIIRTLGVKGGLGYAYEYGGSTVEAMDMESRMTLCNMSIEGGARIGYVNPDETTF 240

Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300
            Y++GR ++PKG ++++A   W + ++D  AT+D VV+ +AEEI+P VTWG NPGQ I V
Sbjct: 241 AYLEGRPYSPKGPEWEEAKKRWLSFRSDPDATYDDVVSFRAEEIAPTVTWGINPGQAIPV 300

Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360
           +  IP      +  ERA AE+ALAYMG +PG P+  V +   FIGSCTN+R+ DLR  A 
Sbjct: 301 DGRIPLLEELPEE-ERAVAEEALAYMGFRPGQPIKGVPVQVAFIGSCTNARLSDLREVAR 359

Query: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP 420
             KG KV  GV+ALVVPGS  V  +AE EG+ ++F EAGFEWR PGCSMCLAMN DRL  
Sbjct: 360 HLKGHKVKKGVRALVVPGSEWVAKKAEEEGIAEVFREAGFEWRNPGCSMCLAMNPDRLEG 419

Query: 421 GERCASTSNRNFEGRQGR-GGRTHLVSPAMAAAAAVTGHFADIRNI 465
            E  AS+SNRN++GR G   GRT L+SP M AAAAVTG  AD R +
Sbjct: 420 DELAASSSNRNYKGRMGSPRGRTVLMSPVMVAAAAVTGEIADAREV 465


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: 701
Number of extensions: 26
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: 466
Length of database: 470
Length adjustment: 33
Effective length of query: 433
Effective length of database: 437
Effective search space:   189221
Effective search space used:   189221
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_053767879.1 BVI061214_RS07580 (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.1626930.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-190  619.2   0.0   2.3e-190  619.1   0.0    1.0  1  NCBI__GCF_001280255.1:WP_053767879.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001280255.1:WP_053767879.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  619.1   0.0  2.3e-190  2.3e-190       1     466 []       1     465 [.       1     465 [. 0.99

  Alignments for each domain:
  == domain 1  score: 619.1 bits;  conditional E-value: 2.3e-190
                             TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve 73 
                                           m ktly+k+++ah v++  n+++ l+id+hl+hevtspqaf  l+  g kvr +++t+at+dh ++t+ r   
  NCBI__GCF_001280255.1:WP_053767879.1   1 MGKTLYDKVWEAHEVRKLRNGQSQLFIDLHLLHEVTSPQAFGMLKDLGLKVRYPHRTFATVDHIVPTHDRTEP 73 
                                           789*******************************************************************999 PP

                             TIGR00170  74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146
                                            ++  a+  +++l +n+ke g+ +fdl s +qgivhv+gp+ glt pg+ti cgdsht+thgafga+afgigt
  NCBI__GCF_001280255.1:WP_053767879.1  74 FQDPLAQNMLEALRRNTKEHGITFFDLGSGNQGIVHVIGPQLGLTQPGMTIACGDSHTSTHGAFGAVAFGIGT 146
                                           9999********************************************************************* PP

                             TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219
                                           s+v  vlatq+l  ++ k  +i+v+gkl +g+ akd+il ii  +gv+gg gy  e+ g +++++ me+rmt+
  NCBI__GCF_001280255.1:WP_053767879.1 147 SQVRDVLATQSLAAKKLKVRRINVDGKLGPGVYAKDVILHIIRTLGVKGGLGYAYEYGGSTVEAMDMESRMTL 219
                                           ************************************************************************* PP

                             TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292
                                           cnm+ie ga+ g ++pdettf+y+ +r+y+pkg e+e+a + w ++++d++a++d vv++ a++i+p+vtwg+
  NCBI__GCF_001280255.1:WP_053767879.1 220 CNMSIEGGARIGYVNPDETTFAYLEGRPYSPKGPEWEEAKKRWLSFRSDPDATYDDVVSFRAEEIAPTVTWGI 292
                                           ************************************************************************* PP

                             TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365
                                           npgq+++v++ +p  ++l ++ e+a ae alay+g++pg+++k + v+  figsctn+r+ dlr+ a  +kg+
  NCBI__GCF_001280255.1:WP_053767879.1 293 NPGQAIPVDGRIPLLEELPEE-ERAVAEEALAYMGFRPGQPIKGVPVQVAFIGSCTNARLSDLREVARHLKGH 364
                                           *****************9865.89************************************************* PP

                             TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438
                                           kv ++v+ alvvpgs+ v k+ae+eg+ ++f eagfewr++gcs+cl+mn+d+l+  e  as+snrn++gr g
  NCBI__GCF_001280255.1:WP_053767879.1 365 KVKKGVR-ALVVPGSEWVAKKAEEEGIAEVFREAGFEWRNPGCSMCLAMNPDRLEGDELAASSSNRNYKGRMG 436
                                           *******.***************************************************************** PP

                             TIGR00170 439 k.garthlvspamaaaaavagkfvdirel 466
                                              +rt l+sp m aaaav+g+++d re+
  NCBI__GCF_001280255.1:WP_053767879.1 437 SpRGRTVLMSPVMVAAAAVTGEIADAREV 465
                                           7479**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (470 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: 29.54
//
[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 2024 update 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 original 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