GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argH in Acidovorax sp. GW101-3H11

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate Ac3H11_1632 Argininosuccinate lyase (EC 4.3.2.1)

Query= SwissProt::Q9LAE5
         (461 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1632
          Length = 489

 Score =  451 bits (1159), Expect = e-131
 Identities = 234/469 (49%), Positives = 305/469 (65%), Gaps = 11/469 (2%)

Query: 2   TKEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQL 61
           TK Q WS  F   +   + R+ +S+ FD  L + D+ GS AHA+MLA  G+IS+E+   +
Sbjct: 20  TKAQAWSALFSEPMSDLVKRYTSSVFFDKRLWQADIAGSLAHAEMLAAQGVISAEDHASI 79

Query: 62  VAGLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRL 121
             G+ QI  E   G F   +D EDVH  +E RLT++VGD GK+LHT RSRNDQV TD RL
Sbjct: 80  QRGMAQITSEIESGAFEWKLDLEDVHLNIEARLTQLVGDAGKRLHTGRSRNDQVATDVRL 139

Query: 122 YLRDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRD 181
           +LR +I  I   L+E Q  L+D+AE++VE ++PG+THLQ AQPVS  HH+LAY +M +RD
Sbjct: 140 WLRGEIDLIGDLLKELQVSLVDVAEQNVEVILPGFTHLQVAQPVSFGHHMLAYVEMFKRD 199

Query: 182 WERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFL 241
            ER+ DV RR N+ PLG  ALAGTT+P+DR   AK L  + +  NSLD VSDRDFAIEF 
Sbjct: 200 AERMADVRRRTNVLPLGSAALAGTTYPLDRERVAKTLGMEGVCQNSLDAVSDRDFAIEFT 259

Query: 242 CAASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRV 301
            AASL MVH+SRL+EE+I+W S+ F F+ + D   TGSSIMPQKKNPDVPEL RGKTGRV
Sbjct: 260 AAASLCMVHVSRLSEELIIWMSQNFGFIKIADRFTTGSSIMPQKKNPDVPELARGKTGRV 319

Query: 302 FGHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILL-----------RE 350
            GHL  ++ +MKG PLAYNKD QEDKE LFD+V+T+K +L     ++             
Sbjct: 320 VGHLMGLITLMKGQPLAYNKDNQEDKEPLFDTVDTLKDTLRIFAEMVGGQLNPATGKKEG 379

Query: 351 GLEFRTQRLAQAVTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLEL 410
           G+      + QA  + ++ ATD+ADYL  +G+PFR+A+  V   VK +      L +L L
Sbjct: 380 GITVNAPAMEQAALKGYATATDLADYLVKKGLPFRDAHETVAHAVKAATTHACDLSELPL 439

Query: 411 EEWQQLHPAFAADIYEAISPRQVVAARNSHGGTGFVQVSKALIAARAQI 459
              Q  HPA   D+YE +S R  + ARN+ GGT   QV   L   RA++
Sbjct: 440 AVLQGFHPAIEKDVYECLSLRGSLNARNTLGGTAPAQVRTQLARHRARL 488


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: 535
Number of extensions: 16
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: 489
Length adjustment: 33
Effective length of query: 428
Effective length of database: 456
Effective search space:   195168
Effective search space used:   195168
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 Ac3H11_1632 (Argininosuccinate lyase (EC 4.3.2.1))
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.3889.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   3.1e-183  595.8   0.0   3.8e-183  595.6   0.0    1.1  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1632  Argininosuccinate lyase (EC 4.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1632  Argininosuccinate lyase (EC 4.3.2.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  595.6   0.0  3.8e-183  3.8e-183       2     454 ..      25     488 ..      24     489 .] 0.97

  Alignments for each domain:
  == domain 1  score: 595.6 bits;  conditional E-value: 3.8e-183
                                        TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeel 63 
                                                      w+  +++ +++ v+++++s+ fDk+l +aDi gs+ah+++La +g++++e+++ ++++++++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1632  25 WSALFSEPMSDLVKRYTSSVFFDKRLWQADIAGSLAHAEMLAAQGVISAEDHASIQRGMAQI 86 
                                                      888999******************************************************** PP

                                        TIGR00838  64 keevkegklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvke 125
                                                      ++e+++g++e++ d eD+Hl++E++l++ vg d+gk+lhtgrsRnDqvatd+rl+lr +++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1632  87 TSEIESGAFEWKLDLEDVHLNIEARLTQLVG-DAGKRLHTGRSRNDQVATDVRLWLRGEIDL 147
                                                      *******************************.****************************** PP

                                        TIGR00838 126 laealkdllkalvekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkR 187
                                                      + + lk+l+ +lv+ Ae++ve+++pg+tHLq AqP++++Hh+lay+em++rD eR+ d+ +R
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1632 148 IGDLLKELQVSLVDVAEQNVEVILPGFTHLQVAQPVSFGHHMLAYVEMFKRDAERMADVRRR 209
                                                      ************************************************************** PP

                                        TIGR00838 188 vnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsr 249
                                                      +n+ PlGs+Alagt++++dre++a++Lg + v++nsldavsdRDf+iE+ +aa+l+mvh+sr
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1632 210 TNVLPLGSAALAGTTYPLDRERVAKTLGMEGVCQNSLDAVSDRDFAIEFTAAASLCMVHVSR 271
                                                      ************************************************************** PP

                                        TIGR00838 250 laEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltglltilKal 311
                                                      l+Eeli++ s++fgf++++d++++gssimPqKKnpDv El+Rgktgrv+G+l+gl+t++K++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1632 272 LSEELIIWMSQNFGFIKIADRFTTGSSIMPQKKNPDVPELARGKTGRVVGHLMGLITLMKGQ 333
                                                      ************************************************************** PP

                                        TIGR00838 312 PlaYnkDlqEdkealfdalktveellevvtgll............kelkvnkerleeaakkn 361
                                                      PlaYnkD qEdke+lfd+++t++++l++++ ++              ++vn   +e+aa k+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1632 334 PLAYNKDNQEDKEPLFDTVDTLKDTLRIFAEMVggqlnpatgkkeGGITVNAPAMEQAALKG 395
                                                      ********************************9554444444322259************** PP

                                        TIGR00838 362 falatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevl 423
                                                      +a+atdlAdylv+kG+PFR+ahe v ++v++a  +  +l+el+l++lq +++++e+dv+e l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1632 396 YATATDLADYLVKKGLPFRDAHETVAHAVKAATTHACDLSELPLAVLQGFHPAIEKDVYECL 457
                                                      ************************************************************** PP

                                        TIGR00838 424 dleeavekrdakGGtakeevekaieeakael 454
                                                      +l+ ++++r++ GGta+++v+++++  +a+l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1632 458 SLRGSLNARNTLGGTAPAQVRTQLARHRARL 488
                                                      *************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (489 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: 8.80
//
[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