GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Lentibacillus jeotgali Grbi

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_010532011.1 ON01_RS15975 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000224785.1:WP_010532011.1
          Length = 469

 Score =  558 bits (1437), Expect = e-163
 Identities = 275/461 (59%), Positives = 347/461 (75%), Gaps = 4/461 (0%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           +T+ EK++  H+V++   +  L+YID HLVHEVTSPQAF+GLR + R VR+P  TFATMD
Sbjct: 5   ETIVEKIWKNHLVHKEPEKPNLMYIDLHLVHEVTSPQAFEGLRLNNRKVRRPDLTFATMD 64

Query: 63  HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122
           HNV T+ +D+    ++++ QM+ L KNCK+FG+ L D+ HP QGIVHV+GP+ G+T PG 
Sbjct: 65  HNVPTKNRDVIE-DQISQKQMETLRKNCKDFGITLADMFHPDQGIVHVIGPQLGLTQPGK 123

Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182
           TIVCGDSHT+THGAFGALAFGIGTSEVEHVLATQTL Q   KT+ + V+G    G+TAKD
Sbjct: 124 TIVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLWQKPPKTLNVHVEGDLGTGVTAKD 183

Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242
           ++LAII K G   GTG+V+E+ GEAIR+LSMEGRMT+CNM+IE GA+AGL++PDETT  +
Sbjct: 184 LILAIISKFGVRFGTGYVMEYTGEAIRNLSMEGRMTVCNMSIEAGARAGLISPDETTVEF 243

Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302
           ++ + H P+G+ FD+    W  L TDEGA +D  VT++A+EI PQV+WGTNPG  + V+ 
Sbjct: 244 LRDKPHVPQGEAFDEKAREWLALATDEGAEYDETVTIKADEIEPQVSWGTNPGMCVPVSG 303

Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362
           + PD     +        +AL YMGL+   P+  + ID VFIGSCTNSRI DLR AA++ 
Sbjct: 304 STPD---VNESDNHDDVARALEYMGLEENQPIQSIDIDHVFIGSCTNSRITDLRKAAKVV 360

Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422
           +G +V   V+A+VVPGS   K QAE EGLD IF EAGFEWR  GCSMCLAMN+D + PG 
Sbjct: 361 EGHQVNDDVRAIVVPGSFGTKLQAEKEGLDAIFKEAGFEWREAGCSMCLAMNDDVVPPGG 420

Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
           RCASTSNRNFEGRQG G RTHLVSP MAAAAA+ GHF D+R
Sbjct: 421 RCASTSNRNFEGRQGNGARTHLVSPEMAAAAAIEGHFVDVR 461


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: 753
Number of extensions: 28
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: 469
Length adjustment: 33
Effective length of query: 433
Effective length of database: 436
Effective search space:   188788
Effective search space used:   188788
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_010532011.1 ON01_RS15975 (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.4130743.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     3e-234  763.7   0.1   3.5e-234  763.5   0.1    1.0  1  NCBI__GCF_000224785.1:WP_010532011.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010532011.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  763.5   0.1  3.5e-234  3.5e-234       2     466 .]       4     463 ..       3     463 .. 0.99

  Alignments for each domain:
  == domain 1  score: 763.5 bits;  conditional E-value: 3.5e-234
                             TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdvei 74 
                                           + t++ek++ +h+v+++ ++++l+yid+hlvhevtspqafeglr ++rkvrr+d t+at+dhn++t++rdv i
  NCBI__GCF_000224785.1:WP_010532011.1   4 PETIVEKIWKNHLVHKEPEKPNLMYIDLHLVHEVTSPQAFEGLRLNNRKVRRPDLTFATMDHNVPTKNRDV-I 75 
                                           78*******************************************************************98.6 PP

                             TIGR00170  75 keekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigts 147
                                            ++ ++ q+++l kn+k+fg+ l+d+ + +qgivhv+gp+ glt pgktivcgdsht+thgafgalafgigts
  NCBI__GCF_000224785.1:WP_010532011.1  76 EDQISQKQMETLRKNCKDFGITLADMFHPDQGIVHVIGPQLGLTQPGKTIVCGDSHTSTHGAFGALAFGIGTS 148
                                           78999******************************************************************** PP

                             TIGR00170 148 evehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvc 220
                                           evehvlatqtl+q+ +ktl+++veg l +g+takd+ilaii k gv++gtgyv+e++geair+lsme+rmtvc
  NCBI__GCF_000224785.1:WP_010532011.1 149 EVEHVLATQTLWQKPPKTLNVHVEGDLGTGVTAKDLILAIISKFGVRFGTGYVMEYTGEAIRNLSMEGRMTVC 221
                                           ************************************************************************* PP

                             TIGR00170 221 nmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtn 293
                                           nm+ieaga+agli+pdett e+++d+++ p+g+ f++   +w +l tdega++d++vt++a++i pqv+wgtn
  NCBI__GCF_000224785.1:WP_010532011.1 222 NMSIEAGARAGLISPDETTVEFLRDKPHVPQGEAFDEKAREWLALATDEGAEYDETVTIKADEIEPQVSWGTN 294
                                           ************************************************************************* PP

                             TIGR00170 294 pgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkk 366
                                           pg+ ++v+++ pd +   + +++ ++ +al+y+gle ++++++i +d+vfigsctnsri+dlr+aa+vv g++
  NCBI__GCF_000224785.1:WP_010532011.1 295 PGMCVPVSGSTPDVN---ESDNHDDVARALEYMGLEENQPIQSIDIDHVFIGSCTNSRITDLRKAAKVVEGHQ 364
                                           ************865...566778899********************************************** PP

                             TIGR00170 367 vadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgk 439
                                           v d+v+ a+vvpgs   k qaekegld if eagfewreagcs+cl+mn+dv++++ rcastsnrnfegrqg+
  NCBI__GCF_000224785.1:WP_010532011.1 365 VNDDVR-AIVVPGSFGTKLQAEKEGLDAIFKEAGFEWREAGCSMCLAMNDDVVPPGGRCASTSNRNFEGRQGN 436
                                           ******.****************************************************************** PP

                             TIGR00170 440 garthlvspamaaaaavagkfvdirel 466
                                           garthlvsp maaaaa+ g+fvd+r++
  NCBI__GCF_000224785.1:WP_010532011.1 437 GARTHLVSPEMAAAAAIEGHFVDVRQF 463
                                           *************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (469 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: 20.46
//
[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:

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