Alignments for a candidate for leuC in Desulfarculus baarsii DSM 2075

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Desulfarculus baarsii DSM 2075

Align 3-isopropylmalate dehydratase large subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate WP_013257171.1 DEBA_RS01700 3-isopropylmalate dehydratase large subunit

Query= SwissProt::P15717
         (466 letters)



>NCBI__GCF_000143965.1:WP_013257171.1
          Length = 464

 Score =  592 bits (1525), Expect = e-173
 Identities = 287/462 (62%), Positives = 353/462 (76%)

Query: 4   TLYEKLFDAHVVFEAPNETPLLYIDRHLVHEVTSPQAFDGLRAHHRPVRQPGKTFATMDH 63
           +L +K++DAHVV   P    LLY+DRHLVHEVTSPQAF GLR   R VR+P  TFA  DH
Sbjct: 3   SLIDKIWDAHVVLREPGRPALLYVDRHLVHEVTSPQAFQGLRLAGRRVRRPDLTFAVCDH 62

Query: 64  NVSTQTKDINASGEMARIQMQELIKNCNEFGVELYDLNHPYQGIVHVMGPEQGVTLPGMT 123
            V T ++    + ++A  Q+  L +N  +FGV  + +  P QG++HV+  EQGV LPG T
Sbjct: 63  VVPTDSRQRPLADQVAETQLAALEQNAAQFGVTFFGMEDPRQGVIHVVMAEQGVILPGAT 122

Query: 124 IVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVTGNAAPGITAKDI 183
           + CGDSHTATHGAFGALAFG+GTSEVEH+LATQTL Q + K+M +   G    G++AKD+
Sbjct: 123 VFCGDSHTATHGAFGALAFGVGTSEVEHILATQTLAQAKPKSMAVRFVGQLPAGLSAKDM 182

Query: 184 VLAIIGKTGSAGGTGHVVEFCGDAIRALSMEGRMTLCNMAIEMGAKAGLVAPDETTFNYV 243
            LA IG+ G+AGGTGH+VE+ G A+ ALSMEGRMTLCNM++E GAKAGLVAPD+TTF+Y+
Sbjct: 183 ALAFIGQVGAAGGTGHLVEYMGPAVEALSMEGRMTLCNMSVECGAKAGLVAPDQTTFDYL 242

Query: 244 KGRLHAPKGRDFDEAVEYWKTLKTDDGATFDTVVALRAEEIAPQVTWGTNPGQVISVTDI 303
           +GR  APKG D+DEAV  W+ LK+D  A FD  V +    + PQVTWG NPGQ   ++  
Sbjct: 243 QGRPFAPKGADWDEAVACWRALKSDADAVFDAEVVVDLSGLEPQVTWGINPGQATGLSGR 302

Query: 304 IPDPASFSDPVERASAEKALAYMGLQPGVPLTDVAIDKVFIGSCTNSRIEDLRAAAEVAK 363
           +PDPA+ +DP ++ +A KALAYMGL+PG  + D+A+D VFIGSCTN RI+DLRAAA V K
Sbjct: 303 VPDPAAMADPEQQRAAIKALAYMGLEPGQKIADLAVDYVFIGSCTNGRIQDLRAAAAVVK 362

Query: 364 GRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGER 423
           GRKVAPGV ALVVPGSG V+AQAEAEGLD++FIEAGF+WRL GCSMCLAMN D L  G+R
Sbjct: 363 GRKVAPGVTALVVPGSGLVRAQAEAEGLDRVFIEAGFQWRLAGCSMCLAMNPDVLPSGKR 422

Query: 424 CASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRSI 465
           CASTSNRNFE RQGRGGRTHL SPA AAA+A+ G  AD R++
Sbjct: 423 CASTSNRNFEDRQGRGGRTHLCSPATAAASAIAGRLADARTL 464


Lambda     K      H
   0.318    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: 771
Number of extensions: 24
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: 466
Length of database: 464
Length adjustment: 33
Effective length of query: 433
Effective length of database: 431
Effective search space:   186623
Effective search space used:   186623
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_013257171.1 DEBA_RS01700 (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.1667890.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.2e-225  733.9   0.0   3.6e-225  733.8   0.0    1.0  1  NCBI__GCF_000143965.1:WP_013257171.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000143965.1:WP_013257171.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  733.8   0.0  3.6e-225  3.6e-225       4     465 ..       3     463 ..       1     464 [] 0.99

  Alignments for each domain:
  == domain 1  score: 733.8 bits;  conditional E-value: 3.6e-225
                             TIGR00170   4 tlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveike 76 
                                           +l++k++dahvv ++ +++ lly+drhlvhevtspqaf+glr agr+vrr+d t+a  dh ++t+sr+    +
  NCBI__GCF_000143965.1:WP_013257171.1   3 SLIDKIWDAHVVLREPGRPALLYVDRHLVHEVTSPQAFQGLRLAGRRVRRPDLTFAVCDHVVPTDSRQRPLAD 75 
                                           589********************************************************************** PP

                             TIGR00170  77 ekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsev 149
                                           ++a  q+ +le+n+ +fgv +f++++ +qg++hvv  e+g+ lpg t+ cgdshtathgafgalafg+gtsev
  NCBI__GCF_000143965.1:WP_013257171.1  76 QVAETQLAALEQNAAQFGVTFFGMEDPRQGVIHVVMAEQGVILPGATVFCGDSHTATHGAFGALAFGVGTSEV 148
                                           ************************************************************************* PP

                             TIGR00170 150 ehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnm 222
                                           eh+latqtl qa++k++ ++  g+l  g++akd+ la ig++g+aggtg++ve+ g a+++lsme+rmt+cnm
  NCBI__GCF_000143965.1:WP_013257171.1 149 EHILATQTLAQAKPKSMAVRFVGQLPAGLSAKDMALAFIGQVGAAGGTGHLVEYMGPAVEALSMEGRMTLCNM 221
                                           ************************************************************************* PP

                             TIGR00170 223 aieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpg 295
                                           ++e gakagl+apd+ttf+y+++r++apkg+++++ava w++lk+d +a+fd +v+++ + + pqvtwg+npg
  NCBI__GCF_000143965.1:WP_013257171.1 222 SVECGAKAGLVAPDQTTFDYLQGRPFAPKGADWDEAVACWRALKSDADAVFDAEVVVDLSGLEPQVTWGINPG 294
                                           ************************************************************************* PP

                             TIGR00170 296 qvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkva 368
                                           q+  +++ vpdp+ +adp +++ a+kalay+glepg+k+ d++vd vfigsctn+ri+dlraaa+vvkg+kva
  NCBI__GCF_000143965.1:WP_013257171.1 295 QATGLSGRVPDPAAMADPEQQRAAIKALAYMGLEPGQKIADLAVDYVFIGSCTNGRIQDLRAAAAVVKGRKVA 367
                                           ************************************************************************* PP

                             TIGR00170 369 dnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkga 441
                                           ++v  alvvpgsglv++qae+egld++f+eagf+wr agcs+cl+mn+dvl++++rcastsnrnfe rqg+g+
  NCBI__GCF_000143965.1:WP_013257171.1 368 PGVT-ALVVPGSGLVRAQAEAEGLDRVFIEAGFQWRLAGCSMCLAMNPDVLPSGKRCASTSNRNFEDRQGRGG 439
                                           ***9.******************************************************************** PP

                             TIGR00170 442 rthlvspamaaaaavagkfvdire 465
                                           rthl spa aaa+a+ag+++d r 
  NCBI__GCF_000143965.1:WP_013257171.1 440 RTHLCSPATAAASAIAGRLADART 463
                                           *********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (464 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 27.55
//
[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