Alignments for a candidate for leuC in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Synechococcus elongatus PCC 7942

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate Synpcc7942_1898 Synpcc7942_1898 isopropylmalate isomerase large subunit

Query= uniprot:A0A1X9Z7T5
         (470 letters)



>FitnessBrowser__SynE:Synpcc7942_1898
          Length = 468

 Score =  504 bits (1297), Expect = e-147
 Identities = 253/464 (54%), Positives = 323/464 (69%), Gaps = 1/464 (0%)

Query: 4   TLVEKIWDAHVVKSEEGFPDILYIDTHLIHEVTSPQAFDGLRKRGLPVFRPKQTVATADH 63
           TL +K+WD H V +       L+I  HLIHEVTSPQAF  LR RGL V  P +TVAT DH
Sbjct: 5   TLFDKVWDLHTVATLPSGQTQLFIGLHLIHEVTSPQAFSMLRDRGLTVKFPGRTVATVDH 64

Query: 64  NVPTLNQLLPIKEELSRYQVDMLTKNCAEFGVELYGLGHPFQGIVHVIGPELGITLPGKT 123
            VPT NQ  P  + L+   +  L +NC E G+  Y +G   QGIVHVI PE G+T PG T
Sbjct: 65  IVPTENQARPFADSLAEEMIVTLERNCRENGIRFYNIGSGSQGIVHVIAPEQGLTQPGMT 124

Query: 124 MVCGDSHTSTHGAFGAIAFGIGTSQVEQVFATQCLLQSKPKTMKIEVNGELGKGVGAKDI 183
           + CGDSHTSTHGAFGAIAFGIGTSQV  V A+Q L  SK K  KIEVNGEL  GV AKD+
Sbjct: 125 IACGDSHTSTHGAFGAIAFGIGTSQVRDVLASQTLALSKLKVRKIEVNGELQPGVYAKDV 184

Query: 184 ILYIIAKISAAGGTGYFIEYAGSAIEALSMEARMTICNMSIEMGARGGLIAPDQTTFDYI 243
           IL+II K+   GG GY  E+AGS   A+SME RMT+CNM+IE GAR G + PDQ T+DY+
Sbjct: 185 ILHIIRKLGVKGGVGYAYEFAGSTFAAMSMEERMTVCNMAIEGGARCGYVNPDQITYDYL 244

Query: 244 KGREFAPAGEEWDKALAYWKTLYSDADAKFDSVLTFDAADIAPMITYGTNPGMGMGIQEH 303
           +GREFAP GE WD+A+A+W++L S+ADA++D V+ FDAA+IAP +T+G  PG G+GI E 
Sbjct: 245 QGREFAPQGEAWDRAIAWWESLRSEADAEYDDVVVFDAAEIAPTVTWGITPGQGIGITET 304

Query: 304 IPATGAQPEKEKLSYQKALDYMGFDDDSSLIGKPVDYVFIGSCTNSRIEDLREVADFVKD 363
           IP   +  ++++    +A  YM  +  + L G  VD  FIGSCTN R+ DLRE A   + 
Sbjct: 305 IPTPDSLLDEDRAVAAEAYSYMDLEPGAPLQGTKVDVCFIGSCTNGRLSDLREAAKVAQG 364

Query: 364 KRKADNVTVWIVPGSKQVEQQAKNEGLDKIFEAAGFQLREPGCSACLGMNEDKIPAGKYC 423
           ++ A  +  ++VPGS++V+QQA+ EGLD+IF AAGF+ R+ GCS CL MN DK+   +  
Sbjct: 365 RKVAAGIKAFVVPGSERVKQQAEAEGLDQIFTAAGFEWRQAGCSMCLAMNPDKLEGRQIS 424

Query: 424 VSTSNRNFEGRQGQ-NARTLLASPLTAAAAAVTGKITDVRDLLD 466
            S+SNRNF+GRQG  + RTLL SP   AAAA+ G++TDVR+ L+
Sbjct: 425 ASSSNRNFKGRQGSASGRTLLMSPAMVAAAAIAGEVTDVRNWLN 468


Lambda     K      H
   0.317    0.135    0.399 

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: 607
Number of extensions: 26
Number of successful extensions: 1
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: 470
Length of database: 468
Length adjustment: 33
Effective length of query: 437
Effective length of database: 435
Effective search space:   190095
Effective search space used:   190095
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 Synpcc7942_1898 Synpcc7942_1898 (isopropylmalate isomerase 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.20054.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-197  641.6   0.0   3.8e-197  641.4   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1898  Synpcc7942_1898 isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1898  Synpcc7942_1898 isopropylmalate isomerase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  641.4   0.0  3.8e-197  3.8e-197       4     465 ..       5     465 ..       1     466 [. 0.99

  Alignments for each domain:
  == domain 1  score: 641.4 bits;  conditional E-value: 3.8e-197
                                 TIGR00170   4 tlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdv 72 
                                               tl++k++d h v    ++++ l+i +hl+hevtspqaf  lr +g  v+ +++t+at+dh ++te++  
  lcl|FitnessBrowser__SynE:Synpcc7942_1898   5 TLFDKVWDLHTVATLPSGQTQLFIGLHLIHEVTSPQAFSMLRDRGLTVKFPGRTVATVDHIVPTENQAR 73 
                                               9******************************************************************** PP

                                 TIGR00170  73 eikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgala 141
                                                  ++ a   + +le+n++e g++++++ s +qgivhv+ pe+glt pg+ti cgdsht+thgafga+a
  lcl|FitnessBrowser__SynE:Synpcc7942_1898  74 PFADSLAEEMIVTLERNCRENGIRFYNIGSGSQGIVHVIAPEQGLTQPGMTIACGDSHTSTHGAFGAIA 142
                                               ********************************************************************* PP

                                 TIGR00170 142 fgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageaird 210
                                               fgigts+v  vla+qtl  ++ k  kiev+g+l++g+ akd+il ii k+gv+gg gy  efag ++ +
  lcl|FitnessBrowser__SynE:Synpcc7942_1898 143 FGIGTSQVRDVLASQTLALSKLKVRKIEVNGELQPGVYAKDVILHIIRKLGVKGGVGYAYEFAGSTFAA 211
                                               ********************************************************************* PP

                                 TIGR00170 211 lsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtl 279
                                               +smeermtvcnmaie ga+ g ++pd++t++y+++r++ap+g+ ++ a+a w +l+++ +a++d vv++
  lcl|FitnessBrowser__SynE:Synpcc7942_1898 212 MSMEERMTVCNMAIEGGARCGYVNPDQITYDYLQGREFAPQGEAWDRAIAWWESLRSEADAEYDDVVVF 280
                                               ********************************************************************* PP

                                 TIGR00170 280 eakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsct 348
                                               +a +i+p+vtwg++pgq + ++e++p p+sl d+ ++a a  a++y+ lepg +l+  kvd  figsct
  lcl|FitnessBrowser__SynE:Synpcc7942_1898 281 DAAEIAPTVTWGITPGQGIGITETIPTPDSLLDE-DRAVAAEAYSYMDLEPGAPLQGTKVDVCFIGSCT 348
                                               *******************************998.6889999*************************** PP

                                 TIGR00170 349 nsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnnd 417
                                               n+r+ dlr+aa+v++g+kva ++k a+vvpgs+ vk+qae+egld+if +agfewr+agcs+cl+mn+d
  lcl|FitnessBrowser__SynE:Synpcc7942_1898 349 NGRLSDLREAAKVAQGRKVAAGIK-AFVVPGSERVKQQAEAEGLDQIFTAAGFEWRQAGCSMCLAMNPD 416
                                               ************************.******************************************** PP

                                 TIGR00170 418 vldeyercastsnrnfegrqgk.garthlvspamaaaaavagkfvdire 465
                                               +l+  +  as+snrnf+grqg  ++rt l+spam aaaa+ag+  d+r+
  lcl|FitnessBrowser__SynE:Synpcc7942_1898 417 KLEGRQISASSSNRNFKGRQGSaSGRTLLMSPAMVAAAAIAGEVTDVRN 465
                                               *********************7268***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (468 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.88
//
[ok]

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