GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Ruegeria conchae TW15

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_010437196.1 G7G_RS0100350 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000192475.1:WP_010437196.1
          Length = 464

 Score =  461 bits (1186), Expect = e-134
 Identities = 236/464 (50%), Positives = 308/464 (66%), Gaps = 9/464 (1%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           M++TLY+KL DAH V +  +   L+Y+D H+++E TSPQAF GL   G  V +P    + 
Sbjct: 1   MSRTLYDKLVDAHKVCDLPDGDMLIYVDFHIMNEYTSPQAFSGLDQKGLSVWRPEAHLSV 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
           +DH  +T+ +D +     +++ +  L  NCK+  +  Y L    QGI HV+ PEQG+  P
Sbjct: 61  VDHVNATRQRDPHDAA--SKLLIDNLEANCKKHNIAFYGLGDRRQGIEHVVVPEQGLVAP 118

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180
           GM I CGDSHT T+GAFGAL FGIGTSEVEHVLATQTL+  R KTM + + G  APG TA
Sbjct: 119 GMLIACGDSHTTTYGAFGALGFGIGTSEVEHVLATQTLRYKRLKTMLVNIDGDLAPGATA 178

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KDI++ ++   G+ G  G+ VEF G AIR   M GRMT+CNMA+E+G +A L+  DE   
Sbjct: 179 KDIIMKVVQVVGAGGANGYAVEFSGSAIRSQEMSGRMTICNMAVELGGRAALIGADEKAL 238

Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300
             +K R H+      D     W    +D GA +DTV  + A +I+P V+WGT+P Q + V
Sbjct: 239 EKIKARAHS---GTLDFGGLEW---NSDPGAEYDTVFEINAADIAPIVSWGTSPDQSVPV 292

Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360
           + ++P       P  R +  +AL YMGLK G  +T++ ID  FIGSCTNSRIEDLRAAA 
Sbjct: 293 DGSVPAETEGMTPKAREALNRALGYMGLKAGQAMTDIEIDSAFIGSCTNSRIEDLRAAAS 352

Query: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWR-LPGCSMCLAMNNDRLN 419
           I KG+KVA  V A+VVPGS   + QAE+EG+D++F EAGF+WR   GCSMCLAMN+D   
Sbjct: 353 ILKGKKVAGSVNAIVVPGSTYTRLQAESEGIDRVFKEAGFDWRPESGCSMCLAMNDDIAM 412

Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
            GER AS++NRNFEGRQGRG RTHL+SP M AAAA+ G  AD+R
Sbjct: 413 DGERIASSTNRNFEGRQGRGARTHLMSPEMVAAAAIHGRIADVR 456


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: 653
Number of extensions: 23
Number of successful extensions: 4
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: 464
Length adjustment: 33
Effective length of query: 433
Effective length of database: 431
Effective search space:   186623
Effective search space used:   186623
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_010437196.1 G7G_RS0100350 (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.1929561.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-177  577.2   0.2   1.3e-177  577.0   0.2    1.0  1  NCBI__GCF_000192475.1:WP_010437196.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000192475.1:WP_010437196.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  577.0   0.2  1.3e-177  1.3e-177       1     466 []       1     458 [.       1     458 [. 0.98

  Alignments for each domain:
  == domain 1  score: 577.0 bits;  conditional E-value: 1.3e-177
                             TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve 73 
                                           m++tly+kl dah v +  ++  l+y+d h++ e tspqaf gl ++g  v r++  l+ +dh  +t++rd  
  NCBI__GCF_000192475.1:WP_010437196.1   1 MSRTLYDKLVDAHKVCDLPDGDMLIYVDFHIMNEYTSPQAFSGLDQKGLSVWRPEAHLSVVDHVNATRQRD-- 71 
                                           79*******************************************************************96.. PP

                             TIGR00170  74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146
                                            ++  +kl + +le n+k+  + +++l + +qgi hvv pe+gl  pg+ i cgdsht+t+gafgal fgigt
  NCBI__GCF_000192475.1:WP_010437196.1  72 PHDAASKLLIDNLEANCKKHNIAFYGLGDRRQGIEHVVVPEQGLVAPGMLIACGDSHTTTYGAFGALGFGIGT 144
                                           67999******************************************************************** PP

                             TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219
                                           sevehvlatqtl+ +r kt+ ++++g la+g takdii+ ++  +g+ g  gy vef+g air+  m +rmt+
  NCBI__GCF_000192475.1:WP_010437196.1 145 SEVEHVLATQTLRYKRLKTMLVNIDGDLAPGATAKDIIMKVVQVVGAGGANGYAVEFSGSAIRSQEMSGRMTI 217
                                           ************************************************************************* PP

                             TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292
                                           cnma+e+g +a li  de ++e +k r ++      +    +w    +d+ga++d+v  ++a di+p v+wgt
  NCBI__GCF_000192475.1:WP_010437196.1 218 CNMAVELGGRAALIGADEKALEKIKARAHSGT---LDFGGLEWN---SDPGAEYDTVFEINAADIAPIVSWGT 284
                                           ***************************99853...455667895...8************************* PP

                             TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365
                                           +p+q ++v+++vp+  +   p  ++  ++al y+gl++g+ ++di++d  figsctnsriedlraaa+++kgk
  NCBI__GCF_000192475.1:WP_010437196.1 285 SPDQSVPVDGSVPAETEGMTPKAREALNRALGYMGLKAGQAMTDIEIDSAFIGSCTNSRIEDLRAAASILKGK 357
                                           ************************************************************************* PP

                             TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewr.eagcslclgmnndvldeyercastsnrnfegrq 437
                                           kva +v+ a+vvpgs   + qae eg+d++f eagf+wr e+gcs+cl+mn+d+  ++er as++nrnfegrq
  NCBI__GCF_000192475.1:WP_010437196.1 358 KVAGSVN-AIVVPGSTYTRLQAESEGIDRVFKEAGFDWRpESGCSMCLAMNDDIAMDGERIASSTNRNFEGRQ 429
                                           *******.*******************************889******************************* PP

                             TIGR00170 438 gkgarthlvspamaaaaavagkfvdirel 466
                                           g+garthl+sp m aaaa++g+++d+re+
  NCBI__GCF_000192475.1:WP_010437196.1 430 GRGARTHLMSPEMVAAAAIHGRIADVREF 458
                                           ***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (464 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 32.58
//
[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