Alignments for a candidate for aceA in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Klebsiella michiganensis M5al

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate BWI76_RS01665 BWI76_RS01665 isocitrate lyase

Query= reanno::Koxy:BWI76_RS01665
         (434 letters)



>FitnessBrowser__Koxy:BWI76_RS01665
          Length = 434

 Score =  876 bits (2264), Expect = 0.0
 Identities = 434/434 (100%), Positives = 434/434 (100%)

Query: 1   MKTRTQQIEELNKEWTKPRWEGITRPYSAEDVVKLRGSVNPECTLAQLGAAKMWRLLHGE 60
           MKTRTQQIEELNKEWTKPRWEGITRPYSAEDVVKLRGSVNPECTLAQLGAAKMWRLLHGE
Sbjct: 1   MKTRTQQIEELNKEWTKPRWEGITRPYSAEDVVKLRGSVNPECTLAQLGAAKMWRLLHGE 60

Query: 61  AKKGYINSLGALTGGQALQQAKAGIEAIYLSGWQVAADANLASSMYPDQSLYPANSVPAV 120
           AKKGYINSLGALTGGQALQQAKAGIEAIYLSGWQVAADANLASSMYPDQSLYPANSVPAV
Sbjct: 61  AKKGYINSLGALTGGQALQQAKAGIEAIYLSGWQVAADANLASSMYPDQSLYPANSVPAV 120

Query: 121 VDRINNTFRRADQIQWSAGIELNDPRYTDYFLPIVADAEAGFGGVLNAFELMKSMIEAGA 180
           VDRINNTFRRADQIQWSAGIELNDPRYTDYFLPIVADAEAGFGGVLNAFELMKSMIEAGA
Sbjct: 121 VDRINNTFRRADQIQWSAGIELNDPRYTDYFLPIVADAEAGFGGVLNAFELMKSMIEAGA 180

Query: 181 AAVHFEDQLASVKKCGHMGGKVLVPTQEAIQKLVAARLAADVMGVPTLVIARTDADAADL 240
           AAVHFEDQLASVKKCGHMGGKVLVPTQEAIQKLVAARLAADVMGVPTLVIARTDADAADL
Sbjct: 181 AAVHFEDQLASVKKCGHMGGKVLVPTQEAIQKLVAARLAADVMGVPTLVIARTDADAADL 240

Query: 241 ITSDCDPYDRQFITGDRTSEGFFRTHAGIEQAISRGLAYAPYADLVWCETSTPDLELAKR 300
           ITSDCDPYDRQFITGDRTSEGFFRTHAGIEQAISRGLAYAPYADLVWCETSTPDLELAKR
Sbjct: 241 ITSDCDPYDRQFITGDRTSEGFFRTHAGIEQAISRGLAYAPYADLVWCETSTPDLELAKR 300

Query: 301 FADAIHAKYPGKLLAYNCSPSFNWQKKLDDKTIASFQQQLADMGYKYQFITLAGIHSMWF 360
           FADAIHAKYPGKLLAYNCSPSFNWQKKLDDKTIASFQQQLADMGYKYQFITLAGIHSMWF
Sbjct: 301 FADAIHAKYPGKLLAYNCSPSFNWQKKLDDKTIASFQQQLADMGYKYQFITLAGIHSMWF 360

Query: 361 NMFDLAHAYAQGEGMKHYVEKVQQPEFAAAKDGYTFVSHQQEVGTGYFDKVTTIIQGGTS 420
           NMFDLAHAYAQGEGMKHYVEKVQQPEFAAAKDGYTFVSHQQEVGTGYFDKVTTIIQGGTS
Sbjct: 361 NMFDLAHAYAQGEGMKHYVEKVQQPEFAAAKDGYTFVSHQQEVGTGYFDKVTTIIQGGTS 420

Query: 421 SVTALTGSTEESQF 434
           SVTALTGSTEESQF
Sbjct: 421 SVTALTGSTEESQF 434


Lambda     K      H
   0.318    0.132    0.394 

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: 834
Number of extensions: 9
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: 434
Length of database: 434
Length adjustment: 32
Effective length of query: 402
Effective length of database: 402
Effective search space:   161604
Effective search space used:   161604
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 BWI76_RS01665 BWI76_RS01665 (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.5509.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   7.5e-219  713.4   4.4   1.6e-125  405.4   0.0    2.0  2  lcl|FitnessBrowser__Koxy:BWI76_RS01665  BWI76_RS01665 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS01665  BWI76_RS01665 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.4   0.0  1.6e-125  1.6e-125       1     254 [.       8     255 ..       8     257 .. 0.99
   2 !  309.2   2.0   2.3e-96   2.3e-96     353     527 .]     256     434 .]     256     434 .] 0.99

  Alignments for each domain:
  == domain 1  score: 405.4 bits;  conditional E-value: 1.6e-125
                               TIGR01346   1 veeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGaldpvq 71 
                                             +ee++keW t++rwe+i+r+ysa+dvvklrGsv++e++l++ +a+k+wr+l+ e k k+++++lGal+++q
  lcl|FitnessBrowser__Koxy:BWI76_RS01665   8 IEELNKEW-TKPRWEGITRPYSAEDVVKLRGSVNPECTLAQLGAAKMWRLLHGEAK-KGYINSLGALTGGQ 76 
                                             68******.8*******************************************999.6************* PP

                               TIGR01346  72 vsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkearskakdeee 141
                                             ++qqaka ++a+ylsGWqv++danl+++++Pd+++yPa++vP++v+r++++++++d++q++a+++ +d+  
  lcl|FitnessBrowser__Koxy:BWI76_RS01665  77 ALQQAKAgIEAIYLSGWQVAADANLASSMYPDQSLYPANSVPAVVDRINNTFRRADQIQWSAGIELNDP-- 145
                                             *******************************************************************99.. PP

                               TIGR01346 142 lkelyidylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhlaGkvlvpvqehvnrl 212
                                                 y dy++Pivada+aGfGGvl++f+l+k +ie+Gaa+vh+edql+s+kkCGh++Gkvlvp+qe++++l
  lcl|FitnessBrowser__Koxy:BWI76_RS01665 146 ---RYTDYFLPIVADAEAGFGGVLNAFELMKSMIEAGAAAVHFEDQLASVKKCGHMGGKVLVPTQEAIQKL 213
                                             ...599***************************************************************** PP

                               TIGR01346 213 vaarlaadvmgvetllvartdaeaatlitsdvdardhefivG 254
                                             vaarlaadvmgv+tl++artda+aa+litsd+d++d++fi+G
  lcl|FitnessBrowser__Koxy:BWI76_RS01665 214 VAARLAADVMGVPTLVIARTDADAADLITSDCDPYDRQFITG 255
                                             *****************************************9 PP

  == domain 2  score: 309.2 bits;  conditional E-value: 2.3e-96
                               TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPsfnWdk 423
                                             +rt+eGf+r+++g+e+ai+r+ a+aPyadlvW+etstPdle+ak+fa+++++k+P+kllayn+sPsfnW+k
  lcl|FitnessBrowser__Koxy:BWI76_RS01665 256 DRTSEGFFRTHAGIEQAISRGLAYAPYADLVWCETSTPDLELAKRFADAIHAKYPGKLLAYNCSPSFNWQK 326
                                             59********************************************************************* PP

                               TIGR01346 424 aleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfak.eGmkayvekvqqrel...edGvdvl 490
                                             +l+d++i++f+++l+d+Gyk+qfitlaG+hs+++++fdla+++a+ eGmk+yvekvqq+e+   +dG++++
  lcl|FitnessBrowser__Koxy:BWI76_RS01665 327 KLDDKTIASFQQQLADMGYKYQFITLAGIHSMWFNMFDLAHAYAQgEGMKHYVEKVQQPEFaaaKDGYTFV 397
                                             ***************************************************************9******* PP

                               TIGR01346 491 khqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                             +hq+e+G++yfd++++++qgG+s+++al++s+ee+qf
  lcl|FitnessBrowser__Koxy:BWI76_RS01665 398 SHQQEVGTGYFDKVTTIIQGGTSSVTALTGSTEESQF 434
                                             ************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (434 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: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 2.91
//
[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