Alignments for a candidate for leuC in Enterococcus termitis LMG 8895

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Enterococcus termitis LMG 8895

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_069663817.1 BCR25_RS11875 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_001730305.1:WP_069663817.1
          Length = 458

 Score =  530 bits (1365), Expect = e-155
 Identities = 274/464 (59%), Positives = 333/464 (71%), Gaps = 12/464 (2%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           M KTL++KL++ HVV   E E  LLYI+ HL+HEVTSPQAF+GLR  GR VR+P +TFAT
Sbjct: 1   MGKTLFDKLWEQHVVSGKEGEPQLLYINLHLIHEVTSPQAFEGLREAGRKVRRPDRTFAT 60

Query: 61  MDHNVSTQTKDI-NACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119
           MDHNV T  KDI N    +A+ Q++ L KNC EFG+ L D     QGIVH++GPE G+T 
Sbjct: 61  MDHNVPT--KDIFNITDLVAKKQIEALQKNCDEFGITLCDNGSDRQGIVHMVGPETGLTQ 118

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179
           PG TIVCGDSHTATHGAFGALAFGIGTSEVEHV ATQ + Q + K+M +++ GK A G+ 
Sbjct: 119 PGKTIVCGDSHTATHGAFGALAFGIGTSEVEHVFATQCIWQNKPKSMGVKITGKLAKGVY 178

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
           AKDI+LA+I K G   G GH VEF GE I +L+ME RMT+CNMAIE GAK G++APDE T
Sbjct: 179 AKDIILALIAKYGVDFGVGHAVEFYGETIENLTMEERMTICNMAIEGGAKMGMMAPDEKT 238

Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299
           F YV+GR +AP  KD D A+A WK L +D  AT+D  + L A+E+ P +TWGTNP   I 
Sbjct: 239 FEYVRGREYAP--KDMDAAIAEWKKLPSDPDATYDINLELNADELVPYITWGTNPEMGIP 296

Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
           V    P+       ++  + E+A  YM L+PG   +++ I  VFIGSCTN R+ DL  AA
Sbjct: 297 VTGTFPE-------IKDMNDERAYHYMDLQPGQRPSDIEIGYVFIGSCTNGRLSDLEEAA 349

Query: 360 EIAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419
            I KG++V  G+ A+VVPGS PV+  AE  GLDKIF EAGFEWR PGCSMCL MN D++ 
Sbjct: 350 RIVKGKRVKEGITAIVVPGSRPVRKAAEKIGLDKIFTEAGFEWREPGCSMCLGMNPDQVP 409

Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
            G  CASTSNRNFEGRQG+G RTHL SPAMAA AA+ G F DIR
Sbjct: 410 AGVHCASTSNRNFEGRQGKGARTHLCSPAMAATAALEGTFVDIR 453


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: 708
Number of extensions: 36
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: 466
Length of database: 458
Length adjustment: 33
Effective length of query: 433
Effective length of database: 425
Effective search space:   184025
Effective search space used:   184025
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_069663817.1 BCR25_RS11875 (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.492036.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.2e-220  716.3   0.0   8.3e-220  716.1   0.0    1.0  1  NCBI__GCF_001730305.1:WP_069663817.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069663817.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  716.1   0.0  8.3e-220  8.3e-220       1     465 [.       1     454 [.       1     455 [. 0.99

  Alignments for each domain:
  == domain 1  score: 716.1 bits;  conditional E-value: 8.3e-220
                             TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve 73 
                                           m ktl++kl+++hvv  +e+e++llyi++hl+hevtspqafeglr+agrkvrr+d+t+at+dhn++t+   ++
  NCBI__GCF_001730305.1:WP_069663817.1   1 MGKTLFDKLWEQHVVSGKEGEPQLLYINLHLIHEVTSPQAFEGLREAGRKVRRPDRTFATMDHNVPTKDI-FN 72 
                                           789****************************************************************988.9* PP

                             TIGR00170  74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146
                                           i++ +ak q+++l+kn++efg+ l d  s +qgivh+vgpe glt pgktivcgdshtathgafgalafgigt
  NCBI__GCF_001730305.1:WP_069663817.1  73 ITDLVAKKQIEALQKNCDEFGITLCDNGSDRQGIVHMVGPETGLTQPGKTIVCGDSHTATHGAFGALAFGIGT 145
                                           ************************************************************************* PP

                             TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219
                                           sevehv+atq ++q+++k++ +++ gklakg+ akdiila+i k+gv +g g+ vef ge+i++l+meermt+
  NCBI__GCF_001730305.1:WP_069663817.1 146 SEVEHVFATQCIWQNKPKSMGVKITGKLAKGVYAKDIILALIAKYGVDFGVGHAVEFYGETIENLTMEERMTI 218
                                           ************************************************************************* PP

                             TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292
                                           cnmaie gak g++apde tfeyv++r+yapk  +++ a+a+wk l +d++a++d ++ l+a++++p +twgt
  NCBI__GCF_001730305.1:WP_069663817.1 219 CNMAIEGGAKMGMMAPDEKTFEYVRGREYAPK--DMDAAIAEWKKLPSDPDATYDINLELNADELVPYITWGT 289
                                           *******************************8..889************************************ PP

                             TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365
                                           np++ ++v+++ p+ k++ d       e+a++y+ l+pg++  di++  vfigsctn+r+ dl +aa +vkgk
  NCBI__GCF_001730305.1:WP_069663817.1 290 NPEMGIPVTGTFPEIKDMND-------ERAYHYMDLQPGQRPSDIEIGYVFIGSCTNGRLSDLEEAARIVKGK 355
                                           *************9999987.......69******************************************** PP

                             TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438
                                           +v +++  a+vvpgs +v+k aek gldkif eagfewre+gcs+clgmn+d+++++  castsnrnfegrqg
  NCBI__GCF_001730305.1:WP_069663817.1 356 RVKEGIT-AIVVPGSRPVRKAAEKIGLDKIFTEAGFEWREPGCSMCLGMNPDQVPAGVHCASTSNRNFEGRQG 427
                                           ******9.***************************************************************** PP

                             TIGR00170 439 kgarthlvspamaaaaavagkfvdire 465
                                           kgarthl spamaa+aa+ g fvdir+
  NCBI__GCF_001730305.1:WP_069663817.1 428 KGARTHLCSPAMAATAALEGTFVDIRK 454
                                           *************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (458 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: 00:00:00.00
# Mc/sec: 22.51
//
[ok]

This GapMind analysis is from Jul 26 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