Alignments for a candidate for leuC in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Acidovorax sp. GW101-3H11

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate Ac3H11_1525 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1525
          Length = 473

 Score =  572 bits (1473), Expect = e-167
 Identities = 295/470 (62%), Positives = 346/470 (73%), Gaps = 7/470 (1%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           M +TLY+K++D HVV+  E+ T +LYIDRHLVHEVTSPQAF+GLR  GR V +      T
Sbjct: 1   MGRTLYDKIWDEHVVHTEEDGTSILYIDRHLVHEVTSPQAFEGLREAGRKVWRMSSIVGT 60

Query: 61  MDHNVSTQTKDINACG---EMARIQMQELIKNCKEFG-VELYDLNHPYQGIVHVMGPEQG 116
            DHN  T   +    G    +++ Q+  L  N         +   H  QGIVHV+GPE G
Sbjct: 61  ADHNTPTTGWEHGYDGITDPISKEQITTLNDNMATISPAAFFPFMHKRQGIVHVIGPENG 120

Query: 117 VTLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAP 176
            TLPGMT+VCGDSHT+THGAFGALA GIGTSEVEHV+ATQTL   +AK M ++V G  A 
Sbjct: 121 ATLPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVMATQTLLAKKAKNMLVQVDGTLAK 180

Query: 177 GITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPD 236
           G+T KD+VLAIIGK G+AGGTG+ +EF G   R +SMEGRMT+CNMAIE GA+AGLVA D
Sbjct: 181 GVTPKDVVLAIIGKIGTAGGTGYTIEFAGSVFRAMSMEGRMTVCNMAIEGGARAGLVAVD 240

Query: 237 ETTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQ 296
           + T  YVKGR  +P G ++D AVAYWKTL +D  A FDTVV L A EI PQVTWGT+P  
Sbjct: 241 DKTIEYVKGRPLSPTGVEWDQAVAYWKTLHSDADAQFDTVVKLDAAEIQPQVTWGTSPEM 300

Query: 297 VISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLR 356
           V+ ++  +PDP    D  +R + E+AL YM L+PG P+ ++ IDKVFIGSCTNSRIED+R
Sbjct: 301 VLGIDARVPDPDKEKDANKRGAIERALTYMDLQPGKPINDITIDKVFIGSCTNSRIEDMR 360

Query: 357 AAAEIAK--GRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAM 413
            AA + K  GRKVA  V+ ALVVPGSG VK QAE EGLD+IF  AGFEWR PGCSMCLAM
Sbjct: 361 EAAAVVKNLGRKVASNVKLALVVPGSGLVKEQAEREGLDQIFKAAGFEWREPGCSMCLAM 420

Query: 414 NNDRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
           N DRL PGERCASTSNRNFEGRQG GGRTHLVSPAMAAAAAV GHF DIR
Sbjct: 421 NADRLEPGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAVHGHFVDIR 470


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: 729
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: 473
Length adjustment: 33
Effective length of query: 433
Effective length of database: 440
Effective search space:   190520
Effective search space used:   190520
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 Ac3H11_1525 (3-isopropylmalate dehydratase large subunit (EC 4.2.1.33))
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.10658.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
     6e-236  769.3   1.6   6.8e-236  769.2   1.6    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525  3-isopropylmalate dehydratase la


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525  3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  769.2   1.6  6.8e-236  6.8e-236       1     466 []       1     472 [.       1     472 [. 0.98

  Alignments for each domain:
  == domain 1  score: 769.2 bits;  conditional E-value: 6.8e-236
                                        TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatld 62 
                                                      m +tly+k++d+hvv+ +e++t++lyidrhlvhevtspqafeglr+agrkv r+++ ++t d
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525   1 MGRTLYDKIWDEHVVHTEEDGTSILYIDRHLVHEVTSPQAFEGLREAGRKVWRMSSIVGTAD 62 
                                                      789*********************************************************** PP

                                        TIGR00170  63 hnistesr...dveikeekaklqvkeleknvkefg.vklfdlssaeqgivhvvgpeegltlp 120
                                                      hn +t+        i++  +k q+++l+ n+  +    +f + +++qgivhv+gpe+g tlp
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525  63 HNTPTTGWehgYDGITDPISKEQITTLNDNMATISpAAFFPFMHKRQGIVHVIGPENGATLP 124
                                                      *****9873333468999************9988637899********************** PP

                                        TIGR00170 121 gktivcgdshtathgafgalafgigtsevehvlatqtlkqaraktlkievegklakgitakd 182
                                                      g+t+vcgdsht+thgafgala gigtsevehv+atqtl  ++ak++ ++v+g+lakg+t kd
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 125 GMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVMATQTLLAKKAKNMLVQVDGTLAKGVTPKD 186
                                                      ************************************************************** PP

                                        TIGR00170 183 iilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagakagliapdettfeyvk 244
                                                      ++laiigkig+aggtgy +efag ++r++sme+rmtvcnmaie ga+agl+a d+ t+eyvk
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 187 VVLAIIGKIGTAGGTGYTIEFAGSVFRAMSMEGRMTVCNMAIEGGARAGLVAVDDKTIEYVK 248
                                                      ************************************************************** PP

                                        TIGR00170 245 drkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpd 306
                                                      +r+++p g e+++avaywktl++d +a+fd+vv+l+a +i pqvtwgt+p++vl ++  vpd
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 249 GRPLSPTGVEWDQAVAYWKTLHSDADAQFDTVVKLDAAEIQPQVTWGTSPEMVLGIDARVPD 310
                                                      ************************************************************** PP

                                        TIGR00170 307 pksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvk..gkk 366
                                                      p++  d  ++  +e+al+y+ l+pg++++di +dkvfigsctnsried+r+aa+vvk  g+k
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 311 PDKEKDANKRGAIERALTYMDLQPGKPINDITIDKVFIGSCTNSRIEDMREAAAVVKnlGRK 372
                                                      ********************************************************9889** PP

                                        TIGR00170 367 vadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercast 428
                                                      va+nvklalvvpgsglvk+qae+egld+if +agfewre+gcs+cl+mn d+l+++ercast
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 373 VASNVKLALVVPGSGLVKEQAEREGLDQIFKAAGFEWREPGCSMCLAMNADRLEPGERCAST 434
                                                      ************************************************************** PP

                                        TIGR00170 429 snrnfegrqgkgarthlvspamaaaaavagkfvdirel 466
                                                      snrnfegrqg+g+rthlvspamaaaaav+g+fvdir++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1525 435 SNRNFEGRQGAGGRTHLVSPAMAAAAAVHGHFVDIRQF 472
                                                      ************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (473 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.05
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 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 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