GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argG in Pseudomonas fluorescens FW300-N2E3

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate AO353_04105 AO353_04105 argininosuccinate synthase

Query= SwissProt::P59846
         (400 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04105
          Length = 405

 Score =  504 bits (1297), Expect = e-147
 Identities = 249/393 (63%), Positives = 300/393 (76%), Gaps = 3/393 (0%)

Query: 2   KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDL 61
           K+VLAYSGGLDTS+ILKWL++TY  EV+ FTAD+GQGEEVE AR KA   G  +    DL
Sbjct: 6   KVVLAYSGGLDTSVILKWLQDTYNCEVVTFTADLGQGEEVEPARAKAQAMGVKEIYIDDL 65

Query: 62  KEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGND 121
           +EEFVRDFVFPM RA  VYEG YLLGTSIARPLIAK L+ IA E GA+AI+HGATGKGND
Sbjct: 66  REEFVRDFVFPMFRANTVYEGEYLLGTSIARPLIAKRLIEIANETGADAISHGATGKGND 125

Query: 122 QVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEK--PYSMDANLL 179
           QVRFEL AYALKP +KVIAPWREW    R++++ YA  H IP+    +K  PYSMDANLL
Sbjct: 126 QVRFELGAYALKPGVKVIAPWREWDLLSREKLMDYAAKHAIPIERHGKKKSPYSMDANLL 185

Query: 180 HISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALL 239
           HISYEGGVLED W E  + M+R T  PE APD P+Y+E+ +  GD VA++G  ++PA +L
Sbjct: 186 HISYEGGVLEDTWTEHEEDMWRWTVSPENAPDKPQYLELTYRNGDIVALDGVEMTPATVL 245

Query: 240 QRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRD 299
             LN IGG HG+GR+DIVENR+VGMKSRG YETPGGTI+  A RA+ES+TLDREV H +D
Sbjct: 246 ATLNRIGGEHGIGRLDIVENRYVGMKSRGCYETPGGTIMLRAHRAIESITLDREVAHLKD 305

Query: 300 MLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYR 359
            L PKYA L+Y G+W++PER  LQ   D     V GV RLKLYKGNV V GRK+ +SL+ 
Sbjct: 306 ELMPKYASLIYTGYWWSPERLMLQQMIDASQAHVNGVVRLKLYKGNVIVTGRKSDESLFD 365

Query: 360 QDLVSFDEAGG-YDQKDAEGFIKIQALRLRVRA 391
            ++ +F+E GG Y+Q DA GFIK+ ALR+R+ A
Sbjct: 366 ANIATFEEDGGAYNQADAAGFIKLNALRMRIAA 398


Lambda     K      H
   0.319    0.137    0.402 

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: 503
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: 400
Length of database: 405
Length adjustment: 31
Effective length of query: 369
Effective length of database: 374
Effective search space:   138006
Effective search space used:   138006
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate AO353_04105 AO353_04105 (argininosuccinate synthase)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))

# 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/TIGR00032.hmm
# target sequence database:        /tmp/gapView.3988059.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00032  [M=394]
Accession:   TIGR00032
Description: argG: argininosuccinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.5e-146  474.7   0.0   1.7e-146  474.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04105  AO353_04105 argininosuccinate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_04105  AO353_04105 argininosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.5   0.0  1.7e-146  1.7e-146       1     391 [.       6     399 ..       6     402 .. 0.97

  Alignments for each domain:
  == domain 1  score: 474.5 bits;  conditional E-value: 1.7e-146
                                     TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareef 64 
                                                   kvvlaysGGlDtsv+lk+l++  ++ev+++t+d+Gq+ e+++ ++ ka ++G+++ y+ D reef
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04105   6 KVVLAYSGGLDTSVILKWLQDTyNCEVVTFTADLGQG-EEVEPARAKAQAMGVKEIYIDDLREEF 69 
                                                   8*********************99************9.9************************** PP

                                     TIGR00032  65 vkdylfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsil 129
                                                   v+d++f+  +an+vyeg+Yll+t++aRpliak+l+e+a++ ga+a++hG+tgKGnDqvRFel  +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04105  70 VRDFVFPMFRANTVYEGEYLLGTSIARPLIAKRLIEIANETGADAISHGATGKGNDQVRFELGAY 134
                                                   ***************************************************************** PP

                                     TIGR00032 130 llnpdlkviaPvreleli.ReeeieyaaekGievpv..ekekaysiDenllgrsiEageLEdpst 191
                                                   +l+p +kviaP+re++l  Re++++yaa++ i+++   +k+++ys+D nll++s+E+g LEd +t
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04105 135 ALKPGVKVIAPWREWDLLsREKLMDYAAKHAIPIERhgKKKSPYSMDANLLHISYEGGVLEDTWT 199
                                                   ****************987*************99862367889********************** PP

                                     TIGR00032 192 eppediyelvkdpiektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDiv 256
                                                   e  ed+++++++p++++ d+p+++e+++++G  val+g++++p +++ ++n+i+g+hG+Gr+Div
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04105 200 EHEEDMWRWTVSPENAP-DKPQYLELTYRNGDIVALDGVEMTPATVLATLNRIGGEHGIGRLDIV 263
                                                   ***********998888.*********************************************** PP

                                     TIGR00032 257 EdRiiglKsReiYEapalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaeal 321
                                                   E+R++g+KsR++YE+p+ +++++Ah+++e+ +l+++v+++k+    ky+ liY+G+w++p++ +l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04105 264 ENRYVGMKSRGCYETPGGTIMLRAHRAIESITLDREVAHLKDELMPKYASLIYTGYWWSPERLML 328
                                                   ***************************************************************** PP

                                     TIGR00032 322 dalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsfek.dkefdqkdaiGfikirglq 385
                                                   + +i+ +q +v+G+vr+kl+kGn+iv grks++sl+d+++++fe+   +++q da+Gfik+++l+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04105 329 QQMIDASQAHVNGVVRLKLYKGNVIVTGRKSDESLFDANIATFEEdGGAYNQADAAGFIKLNALR 393
                                                   ********************************************9456899************** PP

                                     TIGR00032 386 ikvyre 391
                                                   +++ ++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04105 394 MRIAAN 399
                                                   988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (405 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 20.96
//
[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