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

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.4392.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: 7.62
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis