Alignments for a candidate for aceA in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aceA in Dyella japonica UNC79MFTsu3.2

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate N515DRAFT_4123 N515DRAFT_4123 isocitrate lyase

Query= reanno::pseudo1_N1B4:Pf1N1B4_4042
         (441 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4123
          Length = 433

 Score =  609 bits (1571), Expect = e-179
 Identities = 302/427 (70%), Positives = 353/427 (82%), Gaps = 14/427 (3%)

Query: 15  DWAENPRWKGVTRNYSAADVVRLRGSVQPEHTFAKMGADKLWNLVTQGAKPSFRPEKDFV 74
           DW  NPRW GV RNY+AADVVRLRG+V  EH+ A+ GA++LW  + Q         +DFV
Sbjct: 14  DWQNNPRWNGVRRNYTAADVVRLRGTVPVEHSIARHGAERLWKSLQQ---------EDFV 64

Query: 75  NCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLYPVDSVPTVVKRINN 134
           N +GALTG QA+QQVKAG++AIYLSGWQVAAD N A  MYPDQSLYP +SVP VVKRINN
Sbjct: 65  NALGALTGNQAMQQVKAGLKAIYLSGWQVAADANLAGEMYPDQSLYPANSVPQVVKRINN 124

Query: 135 SFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELMKSMIEAGAAGVHFE 194
           +  RADQ+    G +      ID+  PIVADAEAGFGGVLNA+ELMK+MIEAGA+GVHFE
Sbjct: 125 TLLRADQLHHAEGNDE-----IDWMVPIVADAEAGFGGVLNAFELMKAMIEAGASGVHFE 179

Query: 195 DQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGTPTIILARTDANAADLLTSDCD 254
           DQLASVKKCGHMGGKVLVPT+EAV KLTAARLAADV G PT+++ARTDA+AADLLTSD D
Sbjct: 180 DQLASVKKCGHMGGKVLVPTREAVDKLTAARLAADVLGVPTLLVARTDADAADLLTSDID 239

Query: 255 PYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAPFADLIWCETAKPDLDEARRFAEAIK 314
             D+PFVTGERT EGF++VR GLDQAI+RGLAYAP+ADL+WCET+KP+L+EARRFAEAI 
Sbjct: 240 DNDRPFVTGERTVEGFFRVRPGLDQAISRGLAYAPYADLVWCETSKPNLEEARRFAEAIH 299

Query: 315 KEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITLAGIHNMWHSMFNLA 374
            ++P +LL+YNCSPSFNWKKNLDDATIA+FQREL AMGYK QFITLAG H++ + MF+LA
Sbjct: 300 AQFPGKLLAYNCSPSFNWKKNLDDATIARFQRELGAMGYKFQFITLAGFHSLNYGMFDLA 359

Query: 375 HDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTVIQGGTSSVTALTGS 434
           H YAR  M+A+V+LQE+EFA A +G+T V HQ+EVGTGYFD +T  IQ G SS TAL GS
Sbjct: 360 HGYARRQMSAFVELQEREFAAAERGFTAVKHQREVGTGYFDQVTQAIQQGQSSTTALKGS 419

Query: 435 TEEEQFH 441
           TEE QFH
Sbjct: 420 TEEAQFH 426


Lambda     K      H
   0.317    0.131    0.393 

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: 662
Number of extensions: 18
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: 441
Length of database: 433
Length adjustment: 32
Effective length of query: 409
Effective length of database: 401
Effective search space:   164009
Effective search space used:   164009
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 N515DRAFT_4123 N515DRAFT_4123 (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.23446.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   6.5e-193  627.8   4.6   4.9e-109  351.0   0.2    2.0  2  lcl|FitnessBrowser__Dyella79:N515DRAFT_4123  N515DRAFT_4123 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_4123  N515DRAFT_4123 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.0   0.2  4.9e-109  4.9e-109       2     254 ..       9     248 ..       8     250 .. 0.97
   2 !  279.7   0.5     2e-87     2e-87     353     527 .]     249     425 ..     248     425 .. 0.99

  Alignments for each domain:
  == domain 1  score: 351.0 bits;  conditional E-value: 4.9e-109
                                    TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkeskektvsktlGal 67 
                                                  e+i  +W+ ++rw++++r+y+a dvv+lrG+v+ e+ +++++a++lw+ l++e+     +++lGal
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4123   9 EQITLDWQNNPRWNGVRRNYTAADVVRLRGTVPVEHSIARHGAERLWKSLQQEDF----VNALGAL 70 
                                                  678889********************************************98865....8****** PP

                                    TIGR01346  68 dpvqvsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfkallfhdrkqkea 132
                                                  +++q++qq+ka l+a+ylsGWqv++danl++e++Pd+++yPa++vP++v+r++++ll++d+  + +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4123  71 TGNQAMQQVKAgLKAIYLSGWQVAADANLAGEMYPDQSLYPANSVPQVVKRINNTLLRADQLHHAE 136
                                                  *************************************************************98876 PP

                                    TIGR01346 133 rskakdeeelkelyidylvPivadadaGfGGvlavfkltkllierGaagvhledqlssekkCGhla 198
                                                  ++   de       id++vPivada+aGfGGvl++f+l+k++ie+Ga+gvh+edql+s+kkCGh++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4123 137 GN---DE-------IDWMVPIVADAEAGFGGVLNAFELMKAMIEAGASGVHFEDQLASVKKCGHMG 192
                                                  63...44.......9*************************************************** PP

                                    TIGR01346 199 GkvlvpvqehvnrlvaarlaadvmgvetllvartdaeaatlitsdvdardhefivG 254
                                                  Gkvlvp++e+v++l aarlaadv gv+tllvartda+aa+l+tsd+d+ d++f++G
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4123 193 GKVLVPTREAVDKLTAARLAADVLGVPTLLVARTDADAADLLTSDIDDNDRPFVTG 248
                                                  *******************************************************9 PP

  == domain 2  score: 279.7 bits;  conditional E-value: 2e-87
                                    TIGR01346 353 ertreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynlsPs 418
                                                  ert eGf+rv+ g+++ai+r+ a+aPyadlvW+ets+P+leea++fae+++++fP+kllayn+sPs
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4123 249 ERTVEGFFRVRPGLDQAISRGLAYAPYADLVWCETSKPNLEEARRFAEAIHAQFPGKLLAYNCSPS 314
                                                  7***************************************************************** PP

                                    TIGR01346 419 fnWdkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvqqrel. 483
                                                  fnW+k+l+d +i++f++elg++GykfqfitlaG+hs ++++fdla+++a++ m a+ve +q+re+ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4123 315 FNWKKNLDDATIARFQRELGAMGYKFQFITLAGFHSLNYGMFDLAHGYARRQMSAFVE-LQEREFa 379
                                                  **********************************************************.******* PP

                                    TIGR01346 484 ..edGvdvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                                    e+G++++khq+e+G++yfdq+++ +q G s+t+al++s+ee qf
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4123 380 aaERGFTAVKHQREVGTGYFDQVTQAIQQGQSSTTALKGSTEEAQF 425
                                                  999******************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (433 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: 4.75
//
[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