GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Shewanella sp. ANA-3

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate 7026626 Shewana3_3759 isopropylmalate isomerase large subunit (RefSeq)

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__ANA3:7026626
          Length = 474

 Score =  699 bits (1803), Expect = 0.0
 Identities = 340/461 (73%), Positives = 394/461 (85%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+K++DAHVV   E E P++Y+DRHLVHEVTSPQAF GL+  GR +R P KTFATMD
Sbjct: 11  KTLYQKVWDAHVVATPEGEAPIIYVDRHLVHEVTSPQAFSGLKVAGRKLRAPEKTFATMD 70

Query: 63  HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122
           HN ST++  ++A   MAR Q++ L +NCK+FGV LYD++HP QGIVHVMGPE G+TLPG 
Sbjct: 71  HNTSTRSASLDALSPMARTQVETLAQNCKDFGVRLYDIHHPNQGIVHVMGPELGITLPGT 130

Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182
            IVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTL+Q +AKTMKIEV+G+   G+TAKD
Sbjct: 131 VIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLRQLKAKTMKIEVRGQVTDGVTAKD 190

Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242
           IVLAIIGK G  GGTG+VVEFCGEAI  LSMEGRMT+CNMAIEMGAKAG+VAPD+TTF+Y
Sbjct: 191 IVLAIIGKIGMDGGTGYVVEFCGEAIEALSMEGRMTVCNMAIEMGAKAGMVAPDQTTFDY 250

Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302
           ++GR  APKG+D+ +AVA WK L+TD GA FD  V L A  I+PQ+TWGTNPGQV++++ 
Sbjct: 251 LEGREFAPKGEDWAEAVAAWKALKTDVGAEFDATVVLDAANIAPQLTWGTNPGQVVAIDA 310

Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362
            +P+PA  A+P  RAS EKAL Y+GL  G P+T+VAI+KVFIGSCTNSRIEDLR+AA+ A
Sbjct: 311 PVPNPADEANPTIRASMEKALDYIGLTAGTPMTDVAINKVFIGSCTNSRIEDLRSAAKQA 370

Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422
           KGRKVA GV A+VVPGSG VKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMN+DRL  G+
Sbjct: 371 KGRKVASGVTAIVVPGSGQVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNDDRLEAGD 430

Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
           RCASTSNRNFEGRQGRG RTHLVSPAMAAAAA+ GHF DIR
Sbjct: 431 RCASTSNRNFEGRQGRGSRTHLVSPAMAAAAAIAGHFVDIR 471


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: 773
Number of extensions: 15
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: 474
Length adjustment: 33
Effective length of query: 433
Effective length of database: 441
Effective search space:   190953
Effective search space used:   190953
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 7026626 Shewana3_3759 (isopropylmalate isomerase large subunit (RefSeq))
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.20754.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     1e-256  837.8   2.1   1.2e-256  837.6   2.1    1.0  1  lcl|FitnessBrowser__ANA3:7026626  Shewana3_3759 isopropylmalate is


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026626  Shewana3_3759 isopropylmalate isomerase large subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  837.6   2.1  1.2e-256  1.2e-256       2     465 ..      10     472 ..       9     473 .. 1.00

  Alignments for each domain:
  == domain 1  score: 837.6 bits;  conditional E-value: 1.2e-256
                         TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveikeek 78 
                                       +ktly+k++dahvv   e+e++++y+drhlvhevtspqaf gl++agrk+r ++kt+at+dhn st+s  ++++  +
  lcl|FitnessBrowser__ANA3:7026626  10 PKTLYQKVWDAHVVATPEGEAPIIYVDRHLVHEVTSPQAFSGLKVAGRKLRAPEKTFATMDHNTSTRSASLDALSPM 86 
                                       8**************************************************************************** PP

                         TIGR00170  79 aklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsevehvlat 155
                                       a+ qv++l +n+k+fgv+l+d+++ +qgivhv+gpe g+tlpg+ ivcgdshtathgafgalafgigtsevehvlat
  lcl|FitnessBrowser__ANA3:7026626  87 ARTQVETLAQNCKDFGVRLYDIHHPNQGIVHVMGPELGITLPGTVIVCGDSHTATHGAFGALAFGIGTSEVEHVLAT 163
                                       ***************************************************************************** PP

                         TIGR00170 156 qtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagakagl 232
                                       qtl+q +akt+kiev+g++++g+takdi+laiigkig+ ggtgyvvef+geai++lsme+rmtvcnmaie+gakag+
  lcl|FitnessBrowser__ANA3:7026626 164 QTLRQLKAKTMKIEVRGQVTDGVTAKDIVLAIIGKIGMDGGTGYVVEFCGEAIEALSMEGRMTVCNMAIEMGAKAGM 240
                                       ***************************************************************************** PP

                         TIGR00170 233 iapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdpks 309
                                       +apd+ttf+y+ +r++apkg+++ +ava wk+lktd ga+fd +v+l+a +i+pq+twgtnpgqv++++  vp+p++
  lcl|FitnessBrowser__ANA3:7026626 241 VAPDQTTFDYLEGREFAPKGEDWAEAVAAWKALKTDVGAEFDATVVLDAANIAPQLTWGTNPGQVVAIDAPVPNPAD 317
                                       ***************************************************************************** PP

                         TIGR00170 310 ladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkq 386
                                        a+p  +as+ekal+y+gl++gt+++d++++kvfigsctnsriedlr+aa+ +kg+kva++v  a+vvpgsg+vk+q
  lcl|FitnessBrowser__ANA3:7026626 318 EANPTIRASMEKALDYIGLTAGTPMTDVAINKVFIGSCTNSRIEDLRSAAKQAKGRKVASGVT-AIVVPGSGQVKAQ 393
                                       **************************************************************9.************* PP

                         TIGR00170 387 aekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdi 463
                                       ae+egldkif+eagfewr +gcs+cl+mn+d+l++++rcastsnrnfegrqg+g+rthlvspamaaaaa+ag+fvdi
  lcl|FitnessBrowser__ANA3:7026626 394 AEAEGLDKIFIEAGFEWRLPGCSMCLAMNDDRLEAGDRCASTSNRNFEGRQGRGSRTHLVSPAMAAAAAIAGHFVDI 470
                                       ***************************************************************************** PP

                         TIGR00170 464 re 465
                                       r+
  lcl|FitnessBrowser__ANA3:7026626 471 RK 472
                                       97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (474 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: 7.68
//
[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