GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argH in Herbaspirillum seropedicae SmR1

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate HSERO_RS14685 HSERO_RS14685 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>FitnessBrowser__HerbieS:HSERO_RS14685
          Length = 464

 Score =  442 bits (1137), Expect = e-128
 Identities = 224/458 (48%), Positives = 305/458 (66%), Gaps = 1/458 (0%)

Query: 3   KEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLV 62
           K + WS RF   +   + R+ AS+ FD  + + D+ GS AHA+MLAH GIIS+ +  ++ 
Sbjct: 8   KGEAWSARFSEPVSDLVKRYTASVFFDNRMAQVDIQGSLAHAEMLAHQGIISAADYAEIQ 67

Query: 63  AGLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLY 122
            G+ QI+ E   G+F   +D EDVH  +EKRLTE+VGD GK+LHT RSRNDQV TD RLY
Sbjct: 68  RGMAQIKGEIEAGQFEWLLDLEDVHLNIEKRLTELVGDAGKRLHTGRSRNDQVATDIRLY 127

Query: 123 LRDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDW 182
           +R  +  I   LRE +  LLD+AE+H +T++PG+TH+Q AQP++  HH+LAY +M  RD 
Sbjct: 128 MRGAVDDIIGLLRELRLALLDLAEQHADTILPGFTHMQVAQPITFGHHVLAYVEMFGRDA 187

Query: 183 ERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLC 242
           ER+ D  +R+N  PLG  ALAGTTFPIDR   AK L FD++  NSLD VSDRDFAIEF  
Sbjct: 188 ERMIDARKRINRLPLGAAALAGTTFPIDRLRVAKTLGFDDVCRNSLDAVSDRDFAIEFCA 247

Query: 243 AASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVF 302
            A+L+M H+SR++EE+++W S    F+ + D   TGSSIMPQKKNPDVPEL RGKTGRV 
Sbjct: 248 GAALVMTHISRMSEELVIWMSPRVGFIDIADRFCTGSSIMPQKKNPDVPELARGKTGRVN 307

Query: 303 GHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQA 362
           GHL A+L +MKG PLAYNKD QEDKE LFD+V+T+  +L     + R G+  + + +  A
Sbjct: 308 GHLIALLTLMKGQPLAYNKDNQEDKEPLFDTVDTLTDTLRIFADMAR-GISVKPEAMRAA 366

Query: 363 VTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAA 422
             + ++ ATD+ADYL  +G+PFR+A+  V   V+T +  G  L DL L + +        
Sbjct: 367 ALQGYATATDLADYLVKKGLPFRDAHEAVAHAVRTCVDKGCDLADLSLADLRAFSDLIGE 426

Query: 423 DIYEAISPRQVVAARNSHGGTGFVQVSKALIAARAQID 460
           D++  ++    VAAR+  GGT   QV  A+   R +++
Sbjct: 427 DVFAVLTLEGSVAARDHIGGTAPKQVRAAIAQLRKELN 464


Lambda     K      H
   0.320    0.135    0.384 

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: 516
Number of extensions: 18
Number of successful extensions: 2
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: 461
Length of database: 464
Length adjustment: 33
Effective length of query: 428
Effective length of database: 431
Effective search space:   184468
Effective search space used:   184468
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate HSERO_RS14685 HSERO_RS14685 (argininosuccinate lyase)
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))

# 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/TIGR00838.hmm
# target sequence database:        /tmp/gapView.2470465.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00838  [M=455]
Accession:   TIGR00838
Description: argH: argininosuccinate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.8e-189  616.4   0.0   2.1e-189  616.2   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS14685  HSERO_RS14685 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS14685  HSERO_RS14685 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  616.2   0.0  2.1e-189  2.1e-189       2     454 ..      12     463 ..      11     464 .] 1.00

  Alignments for each domain:
  == domain 1  score: 616.2 bits;  conditional E-value: 2.1e-189
                                  TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 
                                                w+ R+++ +++ v++++as+ fD+++a+ Di+gs+ah+++La++gi+++ + ++++++++++k e+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS14685  12 WSARFSEPVSDLVKRYTASVFFDNRMAQVDIQGSLAHAEMLAHQGIISAADYAEIQRGMAQIKGEIEA 79 
                                                9******************************************************************* PP

                                  TIGR00838  70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkal 137
                                                g++e+  d eD+Hl++E++l++ vg d+gk+lhtgrsRnDqvatd+rly+r +v++++  l++l+ al
  lcl|FitnessBrowser__HerbieS:HSERO_RS14685  80 GQFEWLLDLEDVHLNIEKRLTELVG-DAGKRLHTGRSRNDQVATDIRLYMRGAVDDIIGLLRELRLAL 146
                                                *************************.****************************************** PP

                                  TIGR00838 138 vekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfei 205
                                                +++Ae++ +t++pg+tH+q AqPit++Hh+lay+em+ rD eR++da kR+n+ PlG++Alagt+f+i
  lcl|FitnessBrowser__HerbieS:HSERO_RS14685 147 LDLAEQHADTILPGFTHMQVAQPITFGHHVLAYVEMFGRDAERMIDARKRINRLPLGAAALAGTTFPI 214
                                                ******************************************************************** PP

                                  TIGR00838 206 drellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevss 273
                                                dr ++a++LgFd+v++nsldavsdRDf+iE+ + aal+m+h+sr++Eel+++ s  +gf++++d++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS14685 215 DRLRVAKTLGFDDVCRNSLDAVSDRDFAIEFCAGAALVMTHISRMSEELVIWMSPRVGFIDIADRFCT 282
                                                ******************************************************************** PP

                                  TIGR00838 274 gssimPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvt 341
                                                gssimPqKKnpDv El+Rgktgrv+G+l++llt++K++PlaYnkD qEdke+lfd+++t++++l++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS14685 283 GSSIMPQKKNPDVPELARGKTGRVNGHLIALLTLMKGQPLAYNKDNQEDKEPLFDTVDTLTDTLRIFA 350
                                                ******************************************************************** PP

                                  TIGR00838 342 gllkelkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelq 409
                                                 + + + v+ e ++ aa +++a+atdlAdylv+kG+PFR+ahe v ++v+++++kG +l +l+l+ l+
  lcl|FitnessBrowser__HerbieS:HSERO_RS14685 351 DMARGISVKPEAMRAAALQGYATATDLADYLVKKGLPFRDAHEAVAHAVRTCVDKGCDLADLSLADLR 418
                                                ******************************************************************** PP

                                  TIGR00838 410 klsekleedvlevldleeavekrdakGGtakeevekaieeakael 454
                                                ++s  + edv+ vl+le +v++rd +GGta+++v+ ai+++++el
  lcl|FitnessBrowser__HerbieS:HSERO_RS14685 419 AFSDLIGEDVFAVLTLEGSVAARDHIGGTAPKQVRAAIAQLRKEL 463
                                                ****************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (464 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 28.51
//
[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