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.8806.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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.36
//
[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:

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