GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aceA in Pseudomonas fluorescens FW300-N2C3

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate AO356_22080 AO356_22080 isocitrate lyase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_22080
          Length = 441

 Score =  885 bits (2287), Expect = 0.0
 Identities = 435/441 (98%), Positives = 438/441 (99%)

Query: 1   MALTREQQIAALEKDWAENPRWKGVTRNYSAADVVRLRGSVQPEHTFAKMGADKLWNLVT 60
           MALTREQQIAALEKDWAENPRWKGV RNYSAADVVRLRGSVQPEHTFAKMGA+KLWNLVT
Sbjct: 1   MALTREQQIAALEKDWAENPRWKGVKRNYSAADVVRLRGSVQPEHTFAKMGAEKLWNLVT 60

Query: 61  QGAKPSFRPEKDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLY 120
           QGAKP+FRPEKDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLY
Sbjct: 61  QGAKPAFRPEKDFVNCMGALTGGQAVQQVKAGIQAIYLSGWQVAADNNSAESMYPDQSLY 120

Query: 121 PVDSVPTVVKRINNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELM 180
           PVDSVPTVVKRINNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELM
Sbjct: 121 PVDSVPTVVKRINNSFRRADQIQWKAGKNPGDEGYIDYFAPIVADAEAGFGGVLNAYELM 180

Query: 181 KSMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGTPTIILAR 240
           KSMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAG PTIILAR
Sbjct: 181 KSMIEAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGVPTIILAR 240

Query: 241 TDANAADLLTSDCDPYDQPFVTGERTQEGFYKVRAGLDQAIARGLAYAPFADLIWCETAK 300
           TDANAADLLTSDCDPYDQPFVTG RTQEGFYKVRAGLDQAIARGLAYAP+ADLIWCETAK
Sbjct: 241 TDANAADLLTSDCDPYDQPFVTGTRTQEGFYKVRAGLDQAIARGLAYAPYADLIWCETAK 300

Query: 301 PDLDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL 360
           PDLDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL
Sbjct: 301 PDLDEARRFAEAIKKEYPDQLLSYNCSPSFNWKKNLDDATIAKFQRELSAMGYKHQFITL 360

Query: 361 AGIHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTV 420
           AGIHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTV
Sbjct: 361 AGIHNMWHSMFNLAHDYARNDMTAYVKLQEQEFADAAKGYTFVAHQQEVGTGYFDDMTTV 420

Query: 421 IQGGTSSVTALTGSTEEEQFH 441
           IQGGTSSVTALTGSTEEEQFH
Sbjct: 421 IQGGTSSVTALTGSTEEEQFH 441


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: 892
Number of extensions: 12
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: 441
Length of database: 441
Length adjustment: 32
Effective length of query: 409
Effective length of database: 409
Effective search space:   167281
Effective search space used:   167281
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 AO356_22080 AO356_22080 (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.15060.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
     2e-200  652.6   5.2   1.2e-115  372.9   0.1    2.0  2  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080  AO356_22080 isocitrate lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080  AO356_22080 isocitrate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.9   0.1  1.2e-115  1.2e-115       2     254 ..      10     263 ..       9     265 .. 0.97
   2 !  282.2   1.7   3.5e-88   3.5e-88     354     527 .]     265     440 ..     264     440 .. 0.99

  Alignments for each domain:
  == domain 1  score: 372.9 bits;  conditional E-value: 1.2e-115
                                       TIGR01346   2 eeiqkeWdtddrwekikrdysardvvklrGsvreeeylssemakklwrvlkkesk.....ekt 59 
                                                     + ++k+W  ++rw+++kr+ysa dvv+lrGsv++e++ ++++a+klw+++++  k     ek 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080  10 AALEKDWAENPRWKGVKRNYSAADVVRLRGSVQPEHTFAKMGAEKLWNLVTQGAKpafrpEKD 72 
                                                     5689**********************************************9986544444799 PP

                                       TIGR01346  60 vsktlGaldpvqvsqqaka.ldavylsGWqvssdanlsnepgPdladyPadtvPnkverlfka 121
                                                      ++++Gal+++q++qq+ka ++a+ylsGWqv++d+n +++++Pd+++yP+d+vP++v+r++++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080  73 FVNCMGALTGGQAVQQVKAgIQAIYLSGWQVAADNNSAESMYPDQSLYPVDSVPTVVKRINNS 135
                                                     *************************************************************** PP

                                       TIGR01346 122 llfhdrkqkearskakdeeelkelyidylvPivadadaGfGGvlavfkltkllierGaagvhl 184
                                                     ++++d++q++a++++ de      yidy+ Pivada+aGfGGvl++++l+k +ie+Gaagvh+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080 136 FRRADQIQWKAGKNPGDE-----GYIDYFAPIVADAEAGFGGVLNAYELMKSMIEAGAAGVHF 193
                                                     ***************999.....7*************************************** PP

                                       TIGR01346 185 edqlssekkCGhlaGkvlvpvqehvnrlvaarlaadvmgvetllvartdaeaatlitsdvdar 247
                                                     edql+s+kkCGh++Gkvlvp+qe+v++l aarlaadv+gv+t+++artda+aa+l+tsd+d++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080 194 EDQLASVKKCGHMGGKVLVPTQEAVQKLTAARLAADVAGVPTIILARTDANAADLLTSDCDPY 256
                                                     *************************************************************** PP

                                       TIGR01346 248 dhefivG 254
                                                     d++f++G
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080 257 DQPFVTG 263
                                                     ******9 PP

  == domain 2  score: 282.2 bits;  conditional E-value: 3.5e-88
                                       TIGR01346 354 rtreGfyrvkggveaaivrakafaPyadlvWmetstPdleeakefaegvkskfPdkllaynls 416
                                                     rt+eGfy+v++g+++ai+r+ a+aPyadl+W+et++Pdl+ea++fae++k+++Pd+ll+yn+s
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080 265 RTQEGFYKVRAGLDQAIARGLAYAPYADLIWCETAKPDLDEARRFAEAIKKEYPDQLLSYNCS 327
                                                     9************************************************************** PP

                                       TIGR01346 417 PsfnWdkaleddeikkfikelgdlGykfqfitlaGlhsealavfdlakdfakeGmkayvekvq 479
                                                     PsfnW+k+l+d +i+kf++el+++Gyk+qfitlaG+h ++ ++f+la+d+a++ m+ayv+ +q
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080 328 PSFNWKKNLDDATIAKFQRELSAMGYKHQFITLAGIHNMWHSMFNLAHDYARNDMTAYVK-LQ 389
                                                     ***********************************************************8.** PP

                                       TIGR01346 480 qrel...edGvdvlkhqkesGaeyfdqllklvqgGvsataalaksveedqf 527
                                                     ++e+    +G+++++hq+e+G++yfd++++++qgG+s+++al++s+ee+qf
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22080 390 EQEFadaAKGYTFVAHQQEVGTGYFDDMTTVIQGGTSSVTALTGSTEEEQF 440
                                                     ****98889*****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (527 nodes)
Target sequences:                          1  (441 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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 3.85
//
[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