Alignments for a candidate for leuC in Novosphingobium barchaimii LL02

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_059151289.1 V474_RS09685 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_001046635.1:WP_059151289.1
          Length = 478

 Score =  551 bits (1419), Expect = e-161
 Identities = 277/469 (59%), Positives = 346/469 (73%), Gaps = 9/469 (1%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           +TLYEK++DAHVV   ++ T L+YIDRHLVHEV+S QAF+GLR  G PVR+   T A  D
Sbjct: 4   RTLYEKIWDAHVVSSRDDGTSLIYIDRHLVHEVSSAQAFEGLRKAGLPVRRTDLTLAMPD 63

Query: 63  HNVSTQTKDINACGEM-------ARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQ 115
           HNV T T  ++A G++       + IQ+  L  N  EFGV  +    P QGIVHV+GPEQ
Sbjct: 64  HNVPT-TPRVDAAGKLIPIVDPASAIQLAALECNVAEFGVPFFTATSPEQGIVHVVGPEQ 122

Query: 116 GVTLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAA 175
           G TLPG T+VCGDSHTA HGA GALAFGIGT+EVEHVLATQTL+  R+++M+I V+GK  
Sbjct: 123 GFTLPGCTLVCGDSHTAAHGALGALAFGIGTTEVEHVLATQTLRMARSRSMEIRVEGKLG 182

Query: 176 PGITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAP 235
            G++AKD++LA+IG+ G  GG GHV+E+ G     +S+E R+T+ NM+IE GA+AGL AP
Sbjct: 183 HGVSAKDVILAVIGRIGVGGGIGHVIEYRGSVFDAMSIEERLTVANMSIEAGARAGLFAP 242

Query: 236 DETTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPG 295
           DETTF Y+KGR  APKGK +D+AVA W+ L+ D+GA FD  +++ A  I+P VTWGTNP 
Sbjct: 243 DETTFAYLKGRPMAPKGKQWDNAVARWRNLRGDDGAVFDKSISIDASTIAPSVTWGTNPE 302

Query: 296 QVISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDL 355
           QV+S++   P    FAD   RA+  +AL YMG+ PG  + +V +D VFIGSCTNSRIEDL
Sbjct: 303 QVVSIDSAAPRLEDFADEGRRAAVARALDYMGIAPGQAMVDVEVDHVFIGSCTNSRIEDL 362

Query: 356 RAAAEIAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMN 414
           RAAA + +GR ++P +Q A+VVPGSG VK  AEAEGLD IF++AGFEWR PGCS CL MN
Sbjct: 363 RAAARVLEGRHLSPRIQSAIVVPGSGLVKRMAEAEGLDTIFMDAGFEWREPGCSACLGMN 422

Query: 415 NDRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
            D + P  RCASTSNRNF GRQG   RTHL+SPAMAAAA V GH AD+R
Sbjct: 423 PDVIPPLGRCASTSNRNFVGRQGPDARTHLMSPAMAAAAGVAGHLADVR 471


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: 709
Number of extensions: 32
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: 478
Length adjustment: 33
Effective length of query: 433
Effective length of database: 445
Effective search space:   192685
Effective search space used:   192685
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_059151289.1 V474_RS09685 (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.1302323.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.4e-225  732.8   0.0   8.7e-225  732.5   0.0    1.0  1  NCBI__GCF_001046635.1:WP_059151289.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_059151289.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  732.5   0.0  8.7e-225  8.7e-225       2     465 ..       3     472 ..       2     473 .. 0.99

  Alignments for each domain:
  == domain 1  score: 732.5 bits;  conditional E-value: 8.7e-225
                             TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr.... 70 
                                           ++tlyek++dahvv   +++t+l+yidrhlvhev+s qafeglr+ag +vrr+d tla  dhn++t+ r    
  NCBI__GCF_001046635.1:WP_059151289.1   3 PRTLYEKIWDAHVVSSRDDGTSLIYIDRHLVHEVSSAQAFEGLRKAGLPVRRTDLTLAMPDHNVPTTPRvdaa 75 
                                           8******************************************************************998877 PP

                             TIGR00170  71 ..dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgala 141
                                              + i++  + +q+ +le nv efgv++f  +s eqgivhvvgpe+g+tlpg t+vcgdshta+hga+gala
  NCBI__GCF_001046635.1:WP_059151289.1  76 gkLIPIVDPASAIQLAALECNVAEFGVPFFTATSPEQGIVHVVGPEQGFTLPGCTLVCGDSHTAAHGALGALA 148
                                           7678899****************************************************************** PP

                             TIGR00170 142 fgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsme 214
                                           fgigt+evehvlatqtl+ ar+++++i+vegkl +g++akd+ila+ig+igv gg g+v+e+ g +++++s+e
  NCBI__GCF_001046635.1:WP_059151289.1 149 FGIGTTEVEHVLATQTLRMARSRSMEIRVEGKLGHGVSAKDVILAVIGRIGVGGGIGHVIEYRGSVFDAMSIE 221
                                           ************************************************************************* PP

                             TIGR00170 215 ermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispq 287
                                           er+tv nm+ieaga+agl apdettf+y+k+r++apkgk++++ava w+ l+ d+ga+fdk+++++a+ i+p 
  NCBI__GCF_001046635.1:WP_059151289.1 222 ERLTVANMSIEAGARAGLFAPDETTFAYLKGRPMAPKGKQWDNAVARWRNLRGDDGAVFDKSISIDASTIAPS 294
                                           ************************************************************************* PP

                             TIGR00170 288 vtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaae 360
                                           vtwgtnp+qv+s+++  p  +++ad+ ++a + +al+y+g+ pg+ + d++vd+vfigsctnsriedlraaa 
  NCBI__GCF_001046635.1:WP_059151289.1 295 VTWGTNPEQVVSIDSAAPRLEDFADEGRRAAVARALDYMGIAPGQAMVDVEVDHVFIGSCTNSRIEDLRAAAR 367
                                           ************************************************************************* PP

                             TIGR00170 361 vvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnf 433
                                           v+ g+++++ ++ a+vvpgsglvk+ ae+egld if++agfewre+gcs clgmn+dv+++  rcastsnrnf
  NCBI__GCF_001046635.1:WP_059151289.1 368 VLEGRHLSPRIQSAIVVPGSGLVKRMAEAEGLDTIFMDAGFEWREPGCSACLGMNPDVIPPLGRCASTSNRNF 440
                                           ************************************************************************* PP

                             TIGR00170 434 egrqgkgarthlvspamaaaaavagkfvdire 465
                                            grqg  arthl+spamaaaa+vag+++d+r 
  NCBI__GCF_001046635.1:WP_059151289.1 441 VGRQGPDARTHLMSPAMAAAAGVAGHLADVRA 472
                                           ******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (478 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: 00:00:00.01
# Mc/sec: 13.35
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original publication.

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

GapMind for Amino acid biosynthesis