Alignments for a candidate for leuC in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Dechlorosoma suillum PS

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate Dsui_3201 Dsui_3201 3-isopropylmalate dehydratase, large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__PS:Dsui_3201
          Length = 468

 Score =  593 bits (1530), Expect = e-174
 Identities = 298/467 (63%), Positives = 355/467 (76%), Gaps = 2/467 (0%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           M +TLY+KL+  HVV+E  + T L+YIDRHLVHEVTSPQAF+GL+  GR   +     AT
Sbjct: 1   MPQTLYDKLWQNHVVHEEADGTALIYIDRHLVHEVTSPQAFEGLKLAGRKPWRVSSIVAT 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELY-DLNHPYQGIVHVMGPEQGVTL 119
            DHN  T   +      ++R Q++ L  N +E G   Y       QGIVHV+GPE G TL
Sbjct: 61  ADHNTPTDHWEEGIKDPISRQQVETLDANIREVGALAYWPFKDMRQGIVHVVGPENGATL 120

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179
           PGMT+VCGDSHT+THGAF  +A GIGTSEVEHV+ATQ L Q ++K+M I V+GK   G+T
Sbjct: 121 PGMTVVCGDSHTSTHGAFACMAHGIGTSEVEHVMATQCLIQKKSKSMLIRVEGKLGKGVT 180

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
            KD+ LAIIGK G+AGGTG+ +EF G AIR LSMEGRMTLCNMAIE GA+ G VA D+TT
Sbjct: 181 GKDVALAIIGKIGTAGGTGYAIEFGGSAIRGLSMEGRMTLCNMAIEAGARMGFVAVDDTT 240

Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299
            NY+K R  +PKG+ +D AVAYW+TL++DEGA FD  V L+AEEI PQVTWGT+P  V+ 
Sbjct: 241 INYLKDRPFSPKGETWDKAVAYWRTLKSDEGARFDCTVDLKAEEIQPQVTWGTSPEMVVP 300

Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
           +   +PDPA  ADPV+R   E+AL YMGL P + + ++AIDKVFIGSCTNSRIEDLR AA
Sbjct: 301 IGATVPDPAKEADPVKREGMERALQYMGLTPNLEIKKIAIDKVFIGSCTNSRIEDLREAA 360

Query: 360 EIAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRL 418
            + +GR+ A  V+ ALVVPGSG VK QAEAEGLDKIF+ AGFEWR PGCSMCLAMN DRL
Sbjct: 361 AVVRGRQKAANVKLALVVPGSGLVKRQAEAEGLDKIFVAAGFEWREPGCSMCLAMNADRL 420

Query: 419 NPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
            PGERCASTSNRNFEGRQG GGRTHLVSPAMAAAA + GHFAD+R+I
Sbjct: 421 EPGERCASTSNRNFEGRQGPGGRTHLVSPAMAAAAGIAGHFADVRDI 467


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: 738
Number of extensions: 27
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: 468
Length adjustment: 33
Effective length of query: 433
Effective length of database: 435
Effective search space:   188355
Effective search space used:   188355
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 Dsui_3201 Dsui_3201 (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.24934.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.7e-239  780.4   0.3     3e-239  780.2   0.3    1.0  1  lcl|FitnessBrowser__PS:Dsui_3201  Dsui_3201 3-isopropylmalate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3201  Dsui_3201 3-isopropylmalate dehydratase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  780.2   0.3    3e-239    3e-239       1     466 []       1     467 [.       1     467 [. 0.99

  Alignments for each domain:
  == domain 1  score: 780.2 bits;  conditional E-value: 3e-239
                         TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveikee 77 
                                       m++tly+kl+++hvv+e+ ++t l+yidrhlvhevtspqafegl+ agrk  rv++ +at dhn +t+  +  ik+ 
  lcl|FitnessBrowser__PS:Dsui_3201   1 MPQTLYDKLWQNHVVHEEADGTALIYIDRHLVHEVTSPQAFEGLKLAGRKPWRVSSIVATADHNTPTDHWEEGIKDP 77 
                                       89*************************************************************************** PP

                         TIGR00170  78 kaklqvkeleknvkefg.vklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsevehvl 153
                                        ++ qv++l+ n++e+g + ++ +++++qgivhvvgpe+g tlpg+t+vcgdsht+thgaf ++a gigtsevehv+
  lcl|FitnessBrowser__PS:Dsui_3201  78 ISRQQVETLDANIREVGaLAYWPFKDMRQGIVHVVGPENGATLPGMTVVCGDSHTSTHGAFACMAHGIGTSEVEHVM 154
                                       ****************956899******************************************************* PP

                         TIGR00170 154 atqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagaka 230
                                       atq l+q+++k++ i+vegkl kg+t kd+ laiigkig+aggtgy +ef g air lsme+rmt+cnmaieaga+ 
  lcl|FitnessBrowser__PS:Dsui_3201 155 ATQCLIQKKSKSMLIRVEGKLGKGVTGKDVALAIIGKIGTAGGTGYAIEFGGSAIRGLSMEGRMTLCNMAIEAGARM 231
                                       ***************************************************************************** PP

                         TIGR00170 231 gliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdp 307
                                       g++a d+tt++y+kdr+++pkg+ ++kavayw+tlk+dega+fd +v l+a++i pqvtwgt+p++v+++  +vpdp
  lcl|FitnessBrowser__PS:Dsui_3201 232 GFVAVDDTTINYLKDRPFSPKGETWDKAVAYWRTLKSDEGARFDCTVDLKAEEIQPQVTWGTSPEMVVPIGATVPDP 308
                                       ***************************************************************************** PP

                         TIGR00170 308 ksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvk 384
                                       ++ adpv+++++e+al+y+gl+p+ ++k+i++dkvfigsctnsriedlr+aa+vv+g+++a nvklalvvpgsglvk
  lcl|FitnessBrowser__PS:Dsui_3201 309 AKEADPVKREGMERALQYMGLTPNLEIKKIAIDKVFIGSCTNSRIEDLREAAAVVRGRQKAANVKLALVVPGSGLVK 385
                                       ***************************************************************************** PP

                         TIGR00170 385 kqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfv 461
                                       +qae+egldkif++agfewre+gcs+cl+mn d+l+++ercastsnrnfegrqg g+rthlvspamaaaa++ag+f+
  lcl|FitnessBrowser__PS:Dsui_3201 386 RQAEAEGLDKIFVAAGFEWREPGCSMCLAMNADRLEPGERCASTSNRNFEGRQGPGGRTHLVSPAMAAAAGIAGHFA 462
                                       ***************************************************************************** PP

                         TIGR00170 462 direl 466
                                       d+r++
  lcl|FitnessBrowser__PS:Dsui_3201 463 DVRDI 467
                                       ***96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (468 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: 00:00:00.01
# Mc/sec: 12.17
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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