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_010438762.1 G7G_RS0104305 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000192475.1:WP_010438762.1
          Length = 467

 Score =  632 bits (1629), Expect = 0.0
 Identities = 309/464 (66%), Positives = 377/464 (81%), Gaps = 2/464 (0%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+K++DAHV +EA++ T LLYIDRHLVHEVTSPQAF+GLR  GR VR P KT A  D
Sbjct: 4   KTLYDKIWDAHVAHEADDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRKVRAPEKTIAVPD 63

Query: 63  HNVSTQTKDINAC-GEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPG 121
           HNV T    +N      +RIQ++ L KN K+FG+  Y ++   QGIVH++GPEQG TLPG
Sbjct: 64  HNVPTTPDRVNGIENPESRIQVEALDKNAKDFGIHYYPVHDVRQGIVHIVGPEQGWTLPG 123

Query: 122 MTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAK 181
           MT+VCGDSHTATHGAFGALA GIGTSEVEHVLATQTL Q ++K MK+E+ GK  PG+TAK
Sbjct: 124 MTVVCGDSHTATHGAFGALAHGIGTSEVEHVLATQTLIQKKSKNMKVEITGKLQPGVTAK 183

Query: 182 DIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFN 241
           DI LA+IG+TG+AGGTG+V+E+CGEAIRDLSMEGRMT+CNMAIE GA+AGL+APDETTF 
Sbjct: 184 DITLAVIGETGTAGGTGYVIEYCGEAIRDLSMEGRMTVCNMAIEGGARAGLIAPDETTFE 243

Query: 242 YVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVN 301
           YVKGR HAPKG  ++ A+ +WKTL TDEGA FD V+TL+ E+I+P VTWGT+P  V+ + 
Sbjct: 244 YVKGRPHAPKGAQWEAAMDWWKTLYTDEGARFDKVITLRGEDIAPVVTWGTSPEDVLPIT 303

Query: 302 DNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEI 361
            ++P P  F +  +  +A +++ YMGL+ G  L++V ID VFIGSCTN RIEDLRAAAEI
Sbjct: 304 ASVPHPEDF-EGGKVDAARRSIEYMGLEAGQKLSDVEIDTVFIGSCTNGRIEDLRAAAEI 362

Query: 362 AKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPG 421
            KG+K+  G++A+VVPGSG V+AQAE EGL +IF +AGFEWRL GCSMCLAMN D+L PG
Sbjct: 363 LKGKKIKDGMRAMVVPGSGLVRAQAEEEGLAEIFKDAGFEWRLAGCSMCLAMNPDQLQPG 422

Query: 422 ERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           ERCA+TSNRNFEGRQGRGGRTHL+SPAMAAAAA+TG   D+R +
Sbjct: 423 ERCAATSNRNFEGRQGRGGRTHLLSPAMAAAAAITGRLTDVREM 466


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: 805
Number of extensions: 26
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: 467
Length adjustment: 33
Effective length of query: 433
Effective length of database: 434
Effective search space:   187922
Effective search space used:   187922
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_010438762.1 G7G_RS0104305 (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.1609053.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-245  801.4   0.2   1.3e-245  801.1   0.2    1.0  1  NCBI__GCF_000192475.1:WP_010438762.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000192475.1:WP_010438762.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  801.1   0.2  1.3e-245  1.3e-245       2     466 .]       3     466 ..       2     466 .. 0.98

  Alignments for each domain:
  == domain 1  score: 801.1 bits;  conditional E-value: 1.3e-245
                             TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve. 73 
                                           +ktly+k++dahv +ea+++t llyidrhlvhevtspqafeglr agrkvr ++kt+a  dhn++t+   v+ 
  NCBI__GCF_000192475.1:WP_010438762.1   3 PKTLYDKIWDAHVAHEADDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRKVRAPEKTIAVPDHNVPTTPDRVNg 75 
                                           89***************************************************************99877772 PP

                             TIGR00170  74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146
                                           i + ++++qv++l+kn+k+fg++++ +++++qgivh+vgpe+g tlpg+t+vcgdshtathgafgala gigt
  NCBI__GCF_000192475.1:WP_010438762.1  76 IENPESRIQVEALDKNAKDFGIHYYPVHDVRQGIVHIVGPEQGWTLPGMTVVCGDSHTATHGAFGALAHGIGT 148
                                           56679******************************************************************** PP

                             TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219
                                           sevehvlatqtl+q+++k++k+e+ gkl++g+takdi la+ig +g+aggtgyv+e++geairdlsme+rmtv
  NCBI__GCF_000192475.1:WP_010438762.1 149 SEVEHVLATQTLIQKKSKNMKVEITGKLQPGVTAKDITLAVIGETGTAGGTGYVIEYCGEAIRDLSMEGRMTV 221
                                           ************************************************************************* PP

                             TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292
                                           cnmaie ga+agliapdettfeyvk+r++apkg+++e a++ wktl tdega+fdkv+tl ++di+p vtwgt
  NCBI__GCF_000192475.1:WP_010438762.1 222 CNMAIEGGARAGLIAPDETTFEYVKGRPHAPKGAQWEAAMDWWKTLYTDEGARFDKVITLRGEDIAPVVTWGT 294
                                           ************************************************************************* PP

                             TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365
                                           +p++vl+++ +vp+p+++    +   a ++++y+gle+g+kl d+++d vfigsctn+riedlraaae++kgk
  NCBI__GCF_000192475.1:WP_010438762.1 295 SPEDVLPITASVPHPEDFEGG-KVDAARRSIEYMGLEAGQKLSDVEIDTVFIGSCTNGRIEDLRAAAEILKGK 366
                                           ******************764.567789********************************************* PP

                             TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438
                                           k+ d+++ a+vvpgsglv++qae+egl +if +agfewr agcs+cl+mn+d+l+++erca+tsnrnfegrqg
  NCBI__GCF_000192475.1:WP_010438762.1 367 KIKDGMR-AMVVPGSGLVRAQAEEEGLAEIFKDAGFEWRLAGCSMCLAMNPDQLQPGERCAATSNRNFEGRQG 438
                                           *******.***************************************************************** PP

                             TIGR00170 439 kgarthlvspamaaaaavagkfvdirel 466
                                           +g+rthl+spamaaaaa++g++ d+re+
  NCBI__GCF_000192475.1:WP_010438762.1 439 RGGRTHLLSPAMAAAAAITGRLTDVREM 466
                                           **************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (467 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: 30.67
//
[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