GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Leptospirillum ferrooxidans C2-3

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_014449007.1 LFE_RS04110 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000284315.1:WP_014449007.1
          Length = 465

 Score =  602 bits (1552), Expect = e-177
 Identities = 296/464 (63%), Positives = 361/464 (77%), Gaps = 1/464 (0%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           M +TL EK++D HVV E++  T LLYIDR LVHEVTSPQAF+GL+  GR V +P  T A 
Sbjct: 1   MGRTLLEKIWDDHVVTESDGST-LLYIDRQLVHEVTSPQAFEGLKIAGRAVHRPQATLAV 59

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
            DHNV T  +       ++ +Q++ L KN  E+ V ++ ++   QG+VHV+ PEQG TLP
Sbjct: 60  PDHNVPTTGRKKGIEDPISALQVETLTKNAMEYSVPIFTMDDIRQGVVHVIAPEQGFTLP 119

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180
           GMTIVCGDSHT+THGAFGALAFG+GTSEVEHV+ATQTL Q + K+  I+V G    G T+
Sbjct: 120 GMTIVCGDSHTSTHGAFGALAFGVGTSEVEHVMATQTLIQKKPKSFLIKVNGHLPKGSTS 179

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KD++L IIG+ G+ GGTG+V+EF GEA+R+LSME RMTLCNMAIE GA+AG++A DE TF
Sbjct: 180 KDLILYIIGQIGTDGGTGYVLEFSGEAVRELSMEARMTLCNMAIEAGARAGMIAADEVTF 239

Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300
           +Y+KGR  APKG  ++ AV+ WK+L +D  A +D V+ + A  I PQ+TWGTNPG V+ V
Sbjct: 240 SYIKGRPMAPKGDLWEKAVSSWKSLHSDPDAKYDRVLEIDATRIEPQITWGTNPGMVLPV 299

Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360
             +IP P SF D V + +A+ AL YMGL+PG PL+E++ID+VFIGSCTN RIEDLRAAA 
Sbjct: 300 TGSIPSPESFKDEVSKENAKNALKYMGLEPGTPLSEISIDRVFIGSCTNGRIEDLRAAAS 359

Query: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP 420
           I KGRKV+P V A+VVPGSG V  QAE EGLDKIF+EAGFEWR PGCSMCL MN D+L P
Sbjct: 360 IIKGRKVSPSVNAMVVPGSGLVGQQAEKEGLDKIFLEAGFEWREPGCSMCLGMNPDQLLP 419

Query: 421 GERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRN 464
           GERCASTSNRNFEGRQGRGGRTHLVSP MAAAAA+TGHF DIRN
Sbjct: 420 GERCASTSNRNFEGRQGRGGRTHLVSPEMAAAAAITGHFVDIRN 463


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: 751
Number of extensions: 25
Number of successful extensions: 2
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: 465
Length adjustment: 33
Effective length of query: 433
Effective length of database: 432
Effective search space:   187056
Effective search space used:   187056
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_014449007.1 LFE_RS04110 (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.3574365.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-241  787.9   0.0   1.5e-241  787.8   0.0    1.0  1  NCBI__GCF_000284315.1:WP_014449007.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000284315.1:WP_014449007.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  787.8   0.0  1.5e-241  1.5e-241       1     465 [.       1     463 [.       1     464 [. 0.99

  Alignments for each domain:
  == domain 1  score: 787.8 bits;  conditional E-value: 1.5e-241
                             TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve 73 
                                           m +tl+ek++d hvv e+++ ++llyidr lvhevtspqafegl+ agr v r++ tla  dhn++t+ r   
  NCBI__GCF_000284315.1:WP_014449007.1   1 MGRTLLEKIWDDHVVTESDG-STLLYIDRQLVHEVTSPQAFEGLKIAGRAVHRPQATLAVPDHNVPTTGRKKG 72 
                                           789*************9987.579************************************************* PP

                             TIGR00170  74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146
                                           i +  + lqv++l+kn+ e+ v++f +++ +qg+vhv+ pe+g+tlpg+tivcgdsht+thgafgalafg+gt
  NCBI__GCF_000284315.1:WP_014449007.1  73 IEDPISALQVETLTKNAMEYSVPIFTMDDIRQGVVHVIAPEQGFTLPGMTIVCGDSHTSTHGAFGALAFGVGT 145
                                           ************************************************************************* PP

                             TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219
                                           sevehv+atqtl+q+++k++ i+v+g+l kg t+kd+il+iig+ig+ ggtgyv+ef+gea+r+lsme+rmt+
  NCBI__GCF_000284315.1:WP_014449007.1 146 SEVEHVMATQTLIQKKPKSFLIKVNGHLPKGSTSKDLILYIIGQIGTDGGTGYVLEFSGEAVRELSMEARMTL 218
                                           ************************************************************************* PP

                             TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292
                                           cnmaieaga+ag+ia de+tf+y+k+r++apkg+ +ekav+ wk+l++d++ak+d+v+ ++a+ i pq+twgt
  NCBI__GCF_000284315.1:WP_014449007.1 219 CNMAIEAGARAGMIAADEVTFSYIKGRPMAPKGDLWEKAVSSWKSLHSDPDAKYDRVLEIDATRIEPQITWGT 291
                                           ************************************************************************* PP

                             TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365
                                           npg+vl+v++++p+p+s+ d+v+k++a++al+y+glepgt+l +i +d+vfigsctn+riedlraaa+++kg+
  NCBI__GCF_000284315.1:WP_014449007.1 292 NPGMVLPVTGSIPSPESFKDEVSKENAKNALKYMGLEPGTPLSEISIDRVFIGSCTNGRIEDLRAAASIIKGR 364
                                           ************************************************************************* PP

                             TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438
                                           kv+++v+ a+vvpgsglv +qaekegldkifleagfewre+gcs+clgmn+d+l ++ercastsnrnfegrqg
  NCBI__GCF_000284315.1:WP_014449007.1 365 KVSPSVN-AMVVPGSGLVGQQAEKEGLDKIFLEAGFEWREPGCSMCLGMNPDQLLPGERCASTSNRNFEGRQG 436
                                           *******.***************************************************************** PP

                             TIGR00170 439 kgarthlvspamaaaaavagkfvdire 465
                                           +g+rthlvsp maaaaa++g+fvdir+
  NCBI__GCF_000284315.1:WP_014449007.1 437 RGGRTHLVSPEMAAAAAITGHFVDIRN 463
                                           **************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (465 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: 00:00:00.00
# Mc/sec: 21.85
//
[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:

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