Alignments for a candidate for aceA in Kyrpidia tusciae DSM 2912

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Kyrpidia tusciae DSM 2912

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_013075032.1 BTUS_RS05055 isocitrate lyase

Query= BRENDA::Q8RPZ0
         (436 letters)



>NCBI__GCF_000092905.1:WP_013075032.1
          Length = 425

 Score =  593 bits (1529), Expect = e-174
 Identities = 292/421 (69%), Positives = 343/421 (81%), Gaps = 2/421 (0%)

Query: 16  ETAETLAERWATEPRWRDIERTYGAEEVIRLSGSVREEHTLARRGADRLWRQLHELDYVH 75
           + AE L   W T+PRW+ I RTY AE+V+RL GS+R EHTLAR GA+RLW  LH   YV 
Sbjct: 5   QEAEALERSWETDPRWKGIVRTYSAEDVLRLRGSIRIEHTLARMGAERLWHLLHTEPYVP 64

Query: 76  ALGALTGGQAVQQVRAGLQAIYLFGWQVAADANQAGHTYPDQSLYPANSVPQVVRRINNA 135
           ALGALTG QAVQQV+AGL+AIYL GWQVAADAN AG  YPDQSLYPANSVP VV+RIN A
Sbjct: 65  ALGALTGNQAVQQVKAGLKAIYLSGWQVAADANLAGQMYPDQSLYPANSVPHVVKRINQA 124

Query: 136 LLRADQIATAENAGDGTDWLAPIVADAEAGFGGPLNAFELTKAMIEAGAAGIHYEDQLAS 195
           L RADQI   E   D   W APIVADAEAGFGGPLN +EL KAMIEAGAAG+H+EDQLA+
Sbjct: 125 LQRADQIHHMEGKDD-IYWFAPIVADAEAGFGGPLNVYELMKAMIEAGAAGVHFEDQLAA 183

Query: 196 EKKCGHLGGKVLVPTAQHIRTLNAARLAADIADVPTVIIARTDALAASLITSDVDERDAE 255
           EKKCGH+GGKVL+P +Q IR L AARLAAD+  VPT+++ARTDALAA++ITSD+D RD  
Sbjct: 184 EKKCGHMGGKVLIPASQAIRNLTAARLAADVMGVPTILVARTDALAATMITSDIDPRDQG 243

Query: 256 FLTGERTAEGFHRVRNGMAPVIARGLAYAPYADLLWMETGTPDLAQAREFAEAIHAQYPE 315
           F+TGERT+EGF+RVRNG+   IARGLAYAPYAD++W ET  P+L +AR FAEAIHA++P 
Sbjct: 244 FITGERTSEGFYRVRNGLEAAIARGLAYAPYADMIWCETSEPNLEEARLFAEAIHAKFPG 303

Query: 316 QLLAYNCSPSFNWRAALDDDRIAKFQRELGAMGYRFQFITLAGFHSLNHAMFDLARGYAE 375
           +LLAYNCSPSFNW+  LDD  IA FQ++LG MGY+FQF+TLAGFH+LN +MFDLAR Y E
Sbjct: 304 KLLAYNCSPSFNWKRKLDDAAIADFQKKLGQMGYKFQFVTLAGFHALNFSMFDLARQYKE 363

Query: 376 HGMTAYVDLQEREFAAQADGFTAVRHQREVGTGYFDLVSTAVN-PASSTTALSGSTEEEQ 434
            GM AY +LQ+REFA++  G+TA +HQREVG GYFD VS  ++   SSTTAL+GSTEEEQ
Sbjct: 364 RGMAAYAELQQREFASEVYGYTATKHQREVGAGYFDEVSMVISGGTSSTTALTGSTEEEQ 423

Query: 435 F 435
           F
Sbjct: 424 F 424


Lambda     K      H
   0.318    0.131    0.388 

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: 615
Number of extensions: 16
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: 436
Length of database: 425
Length adjustment: 32
Effective length of query: 404
Effective length of database: 393
Effective search space:   158772
Effective search space used:   158772
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_013075032.1 BTUS_RS05055 (isocitrate lyase)
to HMM TIGR01346 (aceA: isocitrate lyase (EC 4.1.3.1))

# 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/TIGR01346.hmm
# target sequence database:        /tmp/gapView.6483.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01346  [M=527]
Accession:   TIGR01346
Description: isocit_lyase: isocitrate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-191  623.0   4.1   2.3e-108  348.8   0.1    2.0  2  lcl|NCBI__GCF_000092905.1:WP_013075032.1  BTUS_RS05055 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013075032.1  BTUS_RS05055 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.8   0.1  2.3e-108  2.3e-108       2     254 ..       8     247 ..       7     248 .. 0.97
   2 !  275.9   0.9   2.9e-86   2.9e-86     353     527 .]     248     424 ..     248     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: 348.8 bits;  conditional E-value: 2.3e-108
                                 TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpv 70 
                                               e +++ W+td+rw++i r ysa+dv +lrGs+r e++l++++a++lw++l++e     ++ +lGal+++
  lcl|NCBI__GCF_000092905.1:WP_013075032.1   8 EALERSWETDPRWKGIVRTYSAEDVLRLRGSIRIEHTLARMGAERLWHLLHTEP----YVPALGALTGN 72 
                                               56899*********************************************9875....69********* PP

                                 TIGR01346  71 qvsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakd 138
                                               q++qq+ka l+a+ylsGWqv++danl+++++Pd+++yPa++vP +v+r+++al+++d++ + ++   kd
  lcl|NCBI__GCF_000092905.1:WP_013075032.1  73 QAVQQVKAgLKAIYLSGWQVAADANLAGQMYPDQSLYPANSVPHVVKRINQALQRADQIHHMEG---KD 138
                                               **********************************************************987655...45 PP

                                 TIGR01346 139 eeelkelyidylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqe 207
                                               +       i ++ Pivada+aGfGG l+v++l+k++ie+Gaagvh+edql++ekkCGh++Gkvl+p  +
  lcl|NCBI__GCF_000092905.1:WP_013075032.1 139 D-------IYWFAPIVADAEAGFGGPLNVYELMKAMIEAGAAGVHFEDQLAAEKKCGHMGGKVLIPASQ 200
                                               5.......89*********************************************************** PP

                                 TIGR01346 208 hvnrlvaarlaadvmgvetllvartdaeaatlitsdvdardhefivG 254
                                               ++++l aarlaadvmgv+t+lvartda aat+itsd+d+rd+ fi+G
  lcl|NCBI__GCF_000092905.1:WP_013075032.1 201 AIRNLTAARLAADVMGVPTILVARTDALAATMITSDIDPRDQGFITG 247
                                               **********************************************9 PP

  == domain 2  score: 275.9 bits;  conditional E-value: 2.9e-86
                                 TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnW 421
                                               ert+eGfyrv++g+eaai+r+ a+aPyad++W+ets P+leea+ fae++++kfP+kllayn+sPsfnW
  lcl|NCBI__GCF_000092905.1:WP_013075032.1 248 ERTSEGFYRVRNGLEAAIARGLAYAPYADMIWCETSEPNLEEARLFAEAIHAKFPGKLLAYNCSPSFNW 316
                                               7******************************************************************** PP

                                 TIGR01346 422 dkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqrel...edGv 487
                                               +++l+d  i++f+k+lg++Gykfqf+tlaG+h+ ++++fdla+++ ++Gm ay+e +qqre+     G+
  lcl|NCBI__GCF_000092905.1:WP_013075032.1 317 KRKLDDAAIADFQKKLGQMGYKFQFVTLAGFHALNFSMFDLARQYKERGMAAYAE-LQQREFaseVYGY 384
                                               *******************************************************.******87778** PP

                                 TIGR01346 488 dvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                               ++ khq+e+Ga+yfd++  ++ gG+s+t+al++s+ee+qf
  lcl|NCBI__GCF_000092905.1:WP_013075032.1 385 TATKHQREVGAGYFDEVSMVISGGTSSTTALTGSTEEEQF 424
                                               ***************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (425 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 4.62
//
[ok]

This GapMind analysis is from Apr 10 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