Aligments for a candidate for argH in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Aligments for a candidate for argH in Desulfovibrio vulgaris Miyazaki F

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate 8499269 DvMF_0048 argininosuccinate lyase (RefSeq)

Query= BRENDA::Q9LAE5
         (461 letters)



>lcl|FitnessBrowser__Miya:8499269 DvMF_0048 argininosuccinate lyase
           (RefSeq)
          Length = 460

 Score =  422 bits (1085), Expect = e-122
 Identities = 220/452 (48%), Positives = 289/452 (63%), Gaps = 1/452 (0%)

Query: 1   MTKEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQ 60
           M +++ W  RF  A    +  +  S+ FD  L   D+ GS+AHA+MLA  G+++++E  +
Sbjct: 1   MAEKKMWGGRFRQATAALVEEYTQSVSFDRALYAQDIAGSKAHARMLAKQGVLTADEAAR 60

Query: 61  LVAGLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTR 120
           +V GL+ +  E   G F    + EDVH  +E RLTE+VGDVGKKLHT RSRNDQV  D R
Sbjct: 61  IVEGLDMVLAEIEGGTFVWRRELEDVHMNIESRLTELVGDVGKKLHTGRSRNDQVALDFR 120

Query: 121 LYLRDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQR 180
           L++ D+I+  +   R+   VL + A +H  TL+PG TH+Q AQPVSL HHLLAY  M +R
Sbjct: 121 LFVSDRIRAWRGLARDLVAVLAERAGEHANTLLPGCTHMQPAQPVSLGHHLLAYAWMLRR 180

Query: 181 DWERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEF 240
           D ERL D  RR  + PLG  ALAGTT+P+D  Y A+ LD    + NS+D VSDRDF +E 
Sbjct: 181 DAERLADCDRRTRVCPLGAAALAGTTYPLDPAYVAEQLDMYGTFRNSMDAVSDRDFVLES 240

Query: 241 LCAASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGR 300
           L   + IM HLSRL EE+I+W++  F FV L D+ ATGSSIMPQKKNPDV E++RGKTGR
Sbjct: 241 LFCGATIMAHLSRLCEEIIIWANPAFGFVRLPDAYATGSSIMPQKKNPDVAEIMRGKTGR 300

Query: 301 VFGHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLA 360
           V+G L AML  +KGLP+ YN+D+QEDKE   D   TV ASLE M  +LRE L F   R+ 
Sbjct: 301 VYGALTAMLTTVKGLPMTYNRDMQEDKEPFLDCDRTVSASLEIMAGMLRE-LGFNEGRMR 359

Query: 361 QAVTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAF 420
            A+   F NAT++ADYL  +G+PFREA++L G  V  +      L++L L + Q +    
Sbjct: 360 AALRAGFLNATELADYLVGKGIPFREAHHLTGAAVALAEERAITLEELPLADLQAICDRI 419

Query: 421 AADIYEAISPRQVVAARNSHGGTGFVQVSKAL 452
             D+Y  + P   VA R   GGTG   V+  L
Sbjct: 420 GDDVYAVLDPAAAVARREMPGGTGPASVAAQL 451


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: 526
Number of extensions: 14
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: 460
Length adjustment: 33
Effective length of query: 428
Effective length of database: 427
Effective search space:   182756
Effective search space used:   182756
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 8499269 DvMF_0048 (argininosuccinate lyase (RefSeq))
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.4823.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   4.4e-183  595.3   0.0   4.9e-183  595.2   0.0    1.0  1  lcl|FitnessBrowser__Miya:8499269  DvMF_0048 argininosuccinate lyas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499269  DvMF_0048 argininosuccinate lyase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  595.2   0.0  4.9e-183  4.9e-183       1     450 [.       6     454 ..       6     459 .. 0.99

  Alignments for each domain:
  == domain 1  score: 595.2 bits;  conditional E-value: 4.9e-183
                         TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelevd 77 
                                       +wggR+++++   v+e+++s+sfD  l+++Di gs+ah+++Lak+g+lt++ea++++e+L+ +  e++ g++ ++ +
  lcl|FitnessBrowser__Miya:8499269   6 MWGGRFRQATAALVEEYTQSVSFDRALYAQDIAGSKAHARMLAKQGVLTADEAARIVEGLDMVLAEIEGGTFVWRRE 82 
                                       6**************************************************************************** PP

                         TIGR00838  78 aeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgytH 154
                                        eD+H+++E++l++ vg dvgkklhtgrsRnDqva d+rl++ d+++  +   +dl+++l+e+A ++ +tl+pg tH
  lcl|FitnessBrowser__Miya:8499269  83 LEDVHMNIESRLTELVG-DVGKKLHTGRSRNDQVALDFRLFVSDRIRAWRGLARDLVAVLAERAGEHANTLLPGCTH 158
                                       *****************.*********************************************************** PP

                         TIGR00838 155 LqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdRD 231
                                       +q AqP++l+Hhllaya+ml+rD eRl d  +R+ ++PlG++Alagt++++d+ ++ae+L      +ns+davsdRD
  lcl|FitnessBrowser__Miya:8499269 159 MQPAQPVSLGHHLLAYAWMLRRDAERLADCDRRTRVCPLGAAALAGTTYPLDPAYVAEQLDMYGTFRNSMDAVSDRD 235
                                       ***************************************************************************** PP

                         TIGR00838 232 fiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltglltil 308
                                       f++E+l+  a +m+hlsrl+Ee+i+++   fgfv l+d++++gssimPqKKnpDvaE++Rgktgrv+G lt++lt++
  lcl|FitnessBrowser__Miya:8499269 236 FVLESLFCGATIMAHLSRLCEEIIIWANPAFGFVRLPDAYATGSSIMPQKKNPDVAEIMRGKTGRVYGALTAMLTTV 312
                                       ***************************************************************************** PP

                         TIGR00838 309 KalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReahei 385
                                       K+lP++Yn+D+qEdke++ d+ +tv+ +le+++g+l+el +n+ r++ a +++f +at+lAdylv kG+PFReah++
  lcl|FitnessBrowser__Miya:8499269 313 KGLPMTYNRDMQEDKEPFLDCDRTVSASLEIMAGMLRELGFNEGRMRAALRAGFLNATELADYLVGKGIPFREAHHL 389
                                       ***************************************************************************** PP

                         TIGR00838 386 vGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieea 450
                                       +G++va a+e+ ++leel+l+ lq++  ++ +dv+ vld+  av++r++ GGt++++v+ +++e+
  lcl|FitnessBrowser__Miya:8499269 390 TGAAVALAEERAITLEELPLADLQAICDRIGDDVYAVLDPAAAVARREMPGGTGPASVAAQLAEL 454
                                       ***********************************************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (460 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: 7.71
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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