GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argG in Pseudomonas fluorescens FW300-N2E2

Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate Pf6N2E2_5590 Argininosuccinate synthase (EC 6.3.4.5)

Query= SwissProt::P59846
         (400 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5590
          Length = 405

 Score =  508 bits (1308), Expect = e-148
 Identities = 251/393 (63%), Positives = 302/393 (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++++ YAE H IP+    +K  PYSMDANLL
Sbjct: 126 QVRFELGAYALKPGVKVIAPWREWDLLSREKLMDYAEKHAIPIERHGKKKSPYSMDANLL 185

Query: 180 HISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALL 239
           HISYEGGVLED W E  + M+R T  PE+APD P+Y+E+ +  GD VA++G  +SPA +L
Sbjct: 186 HISYEGGVLEDTWTEHEEDMWRWTVSPEKAPDTPQYLELTYRNGDIVALDGVEMSPATVL 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: 506
Number of extensions: 19
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 Pf6N2E2_5590 (Argininosuccinate synthase (EC 6.3.4.5))
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.1569.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.7e-146  474.5   0.0     2e-146  474.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5590  Argininosuccinate synthase (EC 6


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5590  Argininosuccinate synthase (EC 6.3.4.5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.3   0.0    2e-146    2e-146       1     391 [.       6     399 ..       6     402 .. 0.97

  Alignments for each domain:
  == domain 1  score: 474.3 bits;  conditional E-value: 2e-146
                                      TIGR00032   1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDaree 63 
                                                    kvvlaysGGlDtsv+lk+l++  ++ev+++t+d+Gq+ e+++ ++ ka ++G+++ y+ D ree
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5590   6 KVVLAYSGGLDTSVILKWLQDTyNCEVVTFTADLGQG-EEVEPARAKAQAMGVKEIYIDDLREE 68 
                                                    8*********************99************9.9************************* PP

                                      TIGR00032  64 fvkdylfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFels 127
                                                    fv+d++f+  +an+vyeg+Yll+t++aRpliak+l+e+a++ ga+a++hG+tgKGnDqvRFel 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5590  69 FVRDFVFPMFRANTVYEGEYLLGTSIARPLIAKRLIEIANETGADAISHGATGKGNDQVRFELG 132
                                                    **************************************************************** PP

                                      TIGR00032 128 illlnpdlkviaPvreleli.ReeeieyaaekGievpv..ekekaysiDenllgrsiEageLEd 188
                                                     ++l+p +kviaP+re++l  Re++++ya+++ i+++   +k+++ys+D nll++s+E+g LEd
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5590 133 AYALKPGVKVIAPWREWDLLsREKLMDYAEKHAIPIERhgKKKSPYSMDANLLHISYEGGVLED 196
                                                    ******************987*************99862367889******************* PP

                                      TIGR00032 189 psteppediyelvkdpiektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGr 252
                                                     +te  ed+++++++p++++ d+p+++e+++++G  val+g++++p +++ ++n+i+g+hG+Gr
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5590 197 TWTEHEEDMWRWTVSPEKAP-DTPQYLELTYRNGDIVALDGVEMSPATVLATLNRIGGEHGIGR 259
                                                    **************988887.******************************************* PP

                                      TIGR00032 253 iDivEdRiiglKsReiYEapalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdp 316
                                                    +DivE+R++g+KsR++YE+p+ +++++Ah+++e+ +l+++v+++k+    ky+ liY+G+w++p
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5590 260 LDIVENRYVGMKSRGCYETPGGTIMLRAHRAIESITLDREVAHLKDELMPKYASLIYTGYWWSP 323
                                                    **************************************************************** PP

                                      TIGR00032 317 laealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsfek.dkefdqkdaiGfi 379
                                                    ++ +l+ +i+ +q +v+G+vr+kl+kGn+iv grks++sl+d+++++fe+   +++q da+Gfi
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5590 324 ERLMLQQMIDASQAHVNGVVRLKLYKGNVIVTGRKSDESLFDANIATFEEdGGAYNQADAAGFI 387
                                                    *************************************************9456899******** PP

                                      TIGR00032 380 kirglqikvyre 391
                                                    k+++l++++ ++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5590 388 KLNALRMRIAAN 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.41
//
[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