GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Azorhizobium caulinodans ORS 571

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_012170633.1 AZC_RS10900 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000010525.1:WP_012170633.1
          Length = 471

 Score =  499 bits (1285), Expect = e-146
 Identities = 250/462 (54%), Positives = 318/462 (68%), Gaps = 3/462 (0%)

Query: 2   AKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATM 61
           A+TL++K++DAHVV + E+   LL+IDRH +HE  S  AFD +   G  + +P  TF   
Sbjct: 6   ARTLFDKVWDAHVVVQREDGQSLLWIDRHFLHE-GSFHAFDKVAGRGASLARPDLTFGVE 64

Query: 62  DHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPG 121
           DH V T+ + ++      R  M++L  N     V L+D++ P QGIVHV+GPEQG+TLPG
Sbjct: 65  DHYVPTRVRQLDLIDPAIRRMMEQLRANTLRHKVRLFDVDDPAQGIVHVVGPEQGLTLPG 124

Query: 122 MTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAK 181
           ++IVCGDSHTATHGAFGALAFGIG SEV HVL TQTL Q R K ++I V+G+ APGI AK
Sbjct: 125 LSIVCGDSHTATHGAFGALAFGIGASEVAHVLMTQTLWQNRPKRLRIRVEGRLAPGIVAK 184

Query: 182 DIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFN 241
           D+ L+II   G+ G  GH +E+ G  +R LSMEGR+TLCN++IE G + G++APD TT +
Sbjct: 185 DVALSIIAAIGADGAAGHAIEYAGSVVRGLSMEGRLTLCNLSIEAGGRCGMIAPDATTLD 244

Query: 242 YVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVN 301
           YV+GR +AP+G  FD A   W  L +D  A FD  V L  + I+P VTWGT+P   + + 
Sbjct: 245 YVRGRPYAPEGALFDAAAEAWLALGSDADAEFDREVVLDGDAIAPIVTWGTSPEDALPIT 304

Query: 302 DNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEI 361
             +PDP    D  + A    A++YM L+PG  L+++A+D+VFIGSCTNSRIEDLRAAA +
Sbjct: 305 ATVPDPERVDDAAKAAHIRDAVSYMDLRPGQRLSDIAVDRVFIGSCTNSRIEDLRAAAAV 364

Query: 362 AKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPG 421
             GR     V  LV PGS  VK QAE EGLD IF  AG EW   GCSMC+ MN D +  G
Sbjct: 365 LAGRSAK--VPGLVSPGSALVKRQAEEEGLDAIFRAAGLEWVEAGCSMCVGMNGDLVPAG 422

Query: 422 ERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
           ERCAST+NRNF+GRQG G RTHL+SPAM AAAAVTGH  D+R
Sbjct: 423 ERCASTTNRNFKGRQGPGARTHLMSPAMVAAAAVTGHLTDMR 464


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: 718
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: 471
Length adjustment: 33
Effective length of query: 433
Effective length of database: 438
Effective search space:   189654
Effective search space used:   189654
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_012170633.1 AZC_RS10900 (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.2386794.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-198  646.3   0.0   1.4e-198  646.1   0.0    1.0  1  NCBI__GCF_000010525.1:WP_012170633.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010525.1:WP_012170633.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  646.1   0.0  1.4e-198  1.4e-198       2     464 ..       6     464 ..       5     466 .. 0.99

  Alignments for each domain:
  == domain 1  score: 646.1 bits;  conditional E-value: 1.4e-198
                             TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdvei 74 
                                           a+tl++k++dahvv + e++++ll+idrh++he  s  af+ +  +g  + r+d t++  dh ++t++r+++ 
  NCBI__GCF_000010525.1:WP_012170633.1   6 ARTLFDKVWDAHVVVQREDGQSLLWIDRHFLHE-GSFHAFDKVAGRGASLARPDLTFGVEDHYVPTRVRQLDL 77 
                                           89*******************************.5899*********************************** PP

                             TIGR00170  75 keekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigts 147
                                            +   ++ +++l  n+ +  v+lfd+++  qgivhvvgpe+gltlpg +ivcgdshtathgafgalafgig+s
  NCBI__GCF_000010525.1:WP_012170633.1  78 IDPAIRRMMEQLRANTLRHKVRLFDVDDPAQGIVHVVGPEQGLTLPGLSIVCGDSHTATHGAFGALAFGIGAS 150
                                           ************************************************************************* PP

                             TIGR00170 148 evehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvc 220
                                           ev hvl tqtl+q+r+k l+i+veg+la+gi akd+ l ii  ig+ g +g+ +e+ag ++r lsme+r+t+c
  NCBI__GCF_000010525.1:WP_012170633.1 151 EVAHVLMTQTLWQNRPKRLRIRVEGRLAPGIVAKDVALSIIAAIGADGAAGHAIEYAGSVVRGLSMEGRLTLC 223
                                           ************************************************************************* PP

                             TIGR00170 221 nmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtn 293
                                           n++ieag + g+iapd tt++yv++r+yap g+ f+ a + w +l +d +a+fd++v+l+++ i+p vtwgt+
  NCBI__GCF_000010525.1:WP_012170633.1 224 NLSIEAGGRCGMIAPDATTLDYVRGRPYAPEGALFDAAAEAWLALGSDADAEFDREVVLDGDAIAPIVTWGTS 296
                                           ************************************************************************* PP

                             TIGR00170 294 pgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkk 366
                                           p+++l+++ +vpdp+ + d  + a++  a++y+ l+pg++l di+vd+vfigsctnsriedlraaa+v+ g+ 
  NCBI__GCF_000010525.1:WP_012170633.1 297 PEDALPITATVPDPERVDDAAKAAHIRDAVSYMDLRPGQRLSDIAVDRVFIGSCTNSRIEDLRAAAAVLAGRS 369
                                           ***********************************************************************95 PP

                             TIGR00170 367 vadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgk 439
                                              +v   lv pgs lvk+qae+egld if +ag+ew eagcs+c+gmn d ++++ercast+nrnf+grqg 
  NCBI__GCF_000010525.1:WP_012170633.1 370 --AKVP-GLVSPGSALVKRQAEEEGLDAIFRAAGLEWVEAGCSMCVGMNGDLVPAGERCASTTNRNFKGRQGP 439
                                           ..4676.89**************************************************************** PP

                             TIGR00170 440 garthlvspamaaaaavagkfvdir 464
                                           garthl+spam aaaav+g++ d+r
  NCBI__GCF_000010525.1:WP_012170633.1 440 GARTHLMSPAMVAAAAVTGHLTDMR 464
                                           ***********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (471 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 27.43
//
[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