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.16603.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.14
//
[ok]

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

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:

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:

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:

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