GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Novosphingobium barchaimii LL02

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_059152441.1 V474_RS16025 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_001046635.1:WP_059152441.1
          Length = 479

 Score =  559 bits (1441), Expect = e-164
 Identities = 281/470 (59%), Positives = 355/470 (75%), Gaps = 7/470 (1%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           +TLY+K++DAHVV   ++ T L+YIDRH+VHEVTSPQAF+ LRA GRPVR+P  T A  D
Sbjct: 6   RTLYQKIWDAHVVDTRDDGTCLIYIDRHIVHEVTSPQAFESLRAAGRPVRRPDLTLAVPD 65

Query: 63  HNV-STQTKDINA----CGEMARIQMQELI-KNCKEFGVELYDLNHPYQGIVHVMGPEQG 116
           HN+ +T  +D N       ++   Q  +L+ KN   FG+         QGIVHV+GPEQG
Sbjct: 66  HNLPTTARRDANGNRIPIADLQSAQQLDLLEKNAPAFGIRYIGDADREQGIVHVVGPEQG 125

Query: 117 VTLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAP 176
            +LPG TIVCGDSHTA +G  GALAFGIGTSEVEHVLATQTL   ++KT ++ V+G    
Sbjct: 126 FSLPGATIVCGDSHTACNGGLGALAFGIGTSEVEHVLATQTLLLKQSKTFEVRVEGTLGA 185

Query: 177 GITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPD 236
           G+T KD++L IIG  G+AGGTG+V+E+ G   R++S+EGR+T+ NM+IE GA+AGLVAPD
Sbjct: 186 GVTPKDVILHIIGLIGTAGGTGYVIEYTGNVFREMSVEGRLTVSNMSIEGGARAGLVAPD 245

Query: 237 ETTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQ 296
           + TF+YVKGR +APKG+++D AVA+WK+L TDEGAT+D  V ++AE+I P +TWGT+P  
Sbjct: 246 DITFDYVKGRPYAPKGEEWDKAVAWWKSLATDEGATYDKSVFIRAEDIQPTITWGTSPED 305

Query: 297 VISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLR 356
             ++   +P P  FAD  +R + + +L YMGL PG+ LTEV +  VFIGSCTNSRIED+R
Sbjct: 306 TSAIGGVVPAPEDFADASKRDAVKHSLEYMGLTPGMKLTEVEVQNVFIGSCTNSRIEDIR 365

Query: 357 AAAEIAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNN 415
           AAAE+ KGR  A  V+ A+VVPGSG VK QAEAEGLDKI I+AG EWR PGCS CLAMN 
Sbjct: 366 AAAEVLKGRHKADNVKWAIVVPGSGLVKEQAEAEGLDKIIIDAGLEWREPGCSACLAMNP 425

Query: 416 DRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           D++ PGERCASTSNRNF GRQG G RTHL+SPAMAAAAAVTG   D+R++
Sbjct: 426 DKVPPGERCASTSNRNFTGRQGPGARTHLMSPAMAAAAAVTGKLTDVRDL 475


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: 755
Number of extensions: 18
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: 479
Length adjustment: 33
Effective length of query: 433
Effective length of database: 446
Effective search space:   193118
Effective search space used:   193118
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_059152441.1 V474_RS16025 (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.1306602.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.1e-229  745.8   0.0   9.3e-229  745.6   0.0    1.0  1  NCBI__GCF_001046635.1:WP_059152441.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_059152441.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  745.6   0.0  9.3e-229  9.3e-229       2     466 .]       5     475 ..       4     475 .. 0.99

  Alignments for each domain:
  == domain 1  score: 745.6 bits;  conditional E-value: 9.3e-229
                             TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr.... 70 
                                           ++tly+k++dahvv   +++t l+yidrh+vhevtspqafe lraagr+vrr+d tla  dhn++t++r    
  NCBI__GCF_001046635.1:WP_059152441.1   5 PRTLYQKIWDAHVVDTRDDGTCLIYIDRHIVHEVTSPQAFESLRAAGRPVRRPDLTLAVPDHNLPTTARrdan 77 
                                           8*****************************************************************9998887 PP

                             TIGR00170  71 ..dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgala 141
                                              + i + ++  q+  lekn+ +fg+++++  + eqgivhvvgpe+g++lpg tivcgdshta  g +gala
  NCBI__GCF_001046635.1:WP_059152441.1  78 gnRIPIADLQSAQQLDLLEKNAPAFGIRYIGDADREQGIVHVVGPEQGFSLPGATIVCGDSHTACNGGLGALA 150
                                           7778899****************************************************************** PP

                             TIGR00170 142 fgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsme 214
                                           fgigtsevehvlatqtl  +++kt++++veg+l  g+t kd+il iig+ig+aggtgyv+e++g+++r++s+e
  NCBI__GCF_001046635.1:WP_059152441.1 151 FGIGTSEVEHVLATQTLLLKQSKTFEVRVEGTLGAGVTPKDVILHIIGLIGTAGGTGYVIEYTGNVFREMSVE 223
                                           ************************************************************************* PP

                             TIGR00170 215 ermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispq 287
                                           +r+tv nm+ie ga+agl+apd++tf+yvk+r+yapkg+e++kava wk+l tdega++dk+v + a+di p+
  NCBI__GCF_001046635.1:WP_059152441.1 224 GRLTVSNMSIEGGARAGLVAPDDITFDYVKGRPYAPKGEEWDKAVAWWKSLATDEGATYDKSVFIRAEDIQPT 296
                                           ************************************************************************* PP

                             TIGR00170 288 vtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaae 360
                                           +twgt+p++  ++ + vp+p+++ad  ++  ++++l+y+gl+pg+kl++++v++vfigsctnsried+raaae
  NCBI__GCF_001046635.1:WP_059152441.1 297 ITWGTSPEDTSAIGGVVPAPEDFADASKRDAVKHSLEYMGLTPGMKLTEVEVQNVFIGSCTNSRIEDIRAAAE 369
                                           ************************************************************************* PP

                             TIGR00170 361 vvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnf 433
                                           v+kg+++adnvk a+vvpgsglvk+qae+egldki+++ag+ewre+gcs cl+mn+d+++++ercastsnrnf
  NCBI__GCF_001046635.1:WP_059152441.1 370 VLKGRHKADNVKWAIVVPGSGLVKEQAEAEGLDKIIIDAGLEWREPGCSACLAMNPDKVPPGERCASTSNRNF 442
                                           ************************************************************************* PP

                             TIGR00170 434 egrqgkgarthlvspamaaaaavagkfvdirel 466
                                            grqg garthl+spamaaaaav+gk+ d+r+l
  NCBI__GCF_001046635.1:WP_059152441.1 443 TGRQGPGARTHLMSPAMAAAAAVTGKLTDVRDL 475
                                           *******************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (479 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: 29.05
//
[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