GapMind for Amino acid biosynthesis

 

Aligments for a candidate for leuC in Synechococcus elongatus PCC 7942

Align 3-isopropylmalate dehydratase large subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate Synpcc7942_1898 Synpcc7942_1898 isopropylmalate isomerase large subunit

Query= SwissProt::P15717
         (466 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_1898 Synpcc7942_1898
           isopropylmalate isomerase large subunit
          Length = 468

 Score =  493 bits (1269), Expect = e-144
 Identities = 251/462 (54%), Positives = 320/462 (69%), Gaps = 2/462 (0%)

Query: 4   TLYEKLFDAHVVFEAPNETPLLYIDRHLVHEVTSPQAFDGLRAHHRPVRQPGKTFATMDH 63
           TL++K++D H V   P+    L+I  HL+HEVTSPQAF  LR     V+ PG+T AT+DH
Sbjct: 5   TLFDKVWDLHTVATLPSGQTQLFIGLHLIHEVTSPQAFSMLRDRGLTVKFPGRTVATVDH 64

Query: 64  NVSTQTKDINASGEMARIQMQELIKNCNEFGVELYDLNHPYQGIVHVMGPEQGVTLPGMT 123
            V T+ +    +  +A   +  L +NC E G+  Y++    QGIVHV+ PEQG+T PGMT
Sbjct: 65  IVPTENQARPFADSLAEEMIVTLERNCRENGIRFYNIGSGSQGIVHVIAPEQGLTQPGMT 124

Query: 124 IVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVTGNAAPGITAKDI 183
           I CGDSHT+THGAFGA+AFGIGTS+V  VLA+QTL   + K  KIEV G   PG+ AKD+
Sbjct: 125 IACGDSHTSTHGAFGAIAFGIGTSQVRDVLASQTLALSKLKVRKIEVNGELQPGVYAKDV 184

Query: 184 VLAIIGKTGSAGGTGHVVEFCGDAIRALSMEGRMTLCNMAIEMGAKAGLVAPDETTFNYV 243
           +L II K G  GG G+  EF G    A+SME RMT+CNMAIE GA+ G V PD+ T++Y+
Sbjct: 185 ILHIIRKLGVKGGVGYAYEFAGSTFAAMSMEERMTVCNMAIEGGARCGYVNPDQITYDYL 244

Query: 244 KGRLHAPKGRDFDEAVEYWKTLKTDDGATFDTVVALRAEEIAPQVTWGTNPGQVISVTDI 303
           +GR  AP+G  +D A+ +W++L+++  A +D VV   A EIAP VTWG  PGQ I +T+ 
Sbjct: 245 QGREFAPQGEAWDRAIAWWESLRSEADAEYDDVVVFDAAEIAPTVTWGITPGQGIGITET 304

Query: 304 IPDPASFSDPVERASAEKALAYMGLQPGVPLTDVAIDKVFIGSCTNSRIEDLRAAAEVAK 363
           IP P S  D  +RA A +A +YM L+PG PL    +D  FIGSCTN R+ DLR AA+VA+
Sbjct: 305 IPTPDSLLDE-DRAVAAEAYSYMDLEPGAPLQGTKVDVCFIGSCTNGRLSDLREAAKVAQ 363

Query: 364 GRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGER 423
           GRKVA G++A VVPGS  VK QAEAEGLD+IF  AGFEWR  GCSMCLAMN D+L   + 
Sbjct: 364 GRKVAAGIKAFVVPGSERVKQQAEAEGLDQIFTAAGFEWRQAGCSMCLAMNPDKLEGRQI 423

Query: 424 CASTSNRNFEGRQG-RGGRTHLVSPAMAAAAAVTGHFADIRS 464
            AS+SNRNF+GRQG   GRT L+SPAM AAAA+ G   D+R+
Sbjct: 424 SASSSNRNFKGRQGSASGRTLLMSPAMVAAAAIAGEVTDVRN 465


Lambda     K      H
   0.318    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: 712
Number of extensions: 29
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: 468
Length adjustment: 33
Effective length of query: 433
Effective length of database: 435
Effective search space:   188355
Effective search space used:   188355
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.5283.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: 00:00:00.03
# Mc/sec: 6.93
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see 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