Alignments for a candidate for argH in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Desulfovibrio vulgaris Hildenborough

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate 206529 DVU1094 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>MicrobesOnline__882:206529
          Length = 460

 Score =  418 bits (1074), Expect = e-121
 Identities = 218/460 (47%), Positives = 296/460 (64%), Gaps = 5/460 (1%)

Query: 1   MTKEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQ 60
           M +++ W  RF+      +  +  S+ +D  L   D+ GS AHA+MLA  G++++EE   
Sbjct: 1   MAEKKMWGGRFKQGTATLVEEYTESVSYDRALYAQDIAGSMAHARMLARQGVLTAEEAAI 60

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

Query: 121 LYLRDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQR 180
           L++ D+++  +   R+  GV++D A +H  TL+PG TH+Q AQPVSLA HLLAY  M +R
Sbjct: 121 LFVSDRVRVWRELGRDLVGVIVDQARQHTATLLPGCTHMQPAQPVSLAQHLLAYAWMLRR 180

Query: 181 DWERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEF 240
           D +RL D  +R  + PLG  ALAGTT+P+D    A  L     + NS+D VSDRDF +E 
Sbjct: 181 DIDRLEDCDKRARVCPLGAAALAGTTYPLDPASVADELGMYGTFRNSMDAVSDRDFVLEA 240

Query: 241 LCAASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGR 300
           L   S+IM HLSRL EE ILW++  F ++ L D+ ATGSSIMPQKKNPDV EL+RGKTGR
Sbjct: 241 LFDGSVIMAHLSRLCEEFILWANPAFGYIFLPDAYATGSSIMPQKKNPDVAELMRGKTGR 300

Query: 301 VFGHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLA 360
           V+G L  ML  +KGLP+ YN+DLQEDKE   D+  TV ASLE M  +LRE + F T R+ 
Sbjct: 301 VYGALTTMLTTVKGLPMTYNRDLQEDKEPFIDADRTVSASLEIMAGMLRE-VRFNTARMR 359

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

Query: 421 AADIYEAISPRQVVAARNSHGGTGFVQVSKALIAARAQID 460
             D+Y  + P   V+ R + GGTG     +++ A  A++D
Sbjct: 420 DEDVYPILEPEAAVSRRETPGGTG----PRSVAAQIAELD 455


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: 521
Number of extensions: 19
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 206529 DVU1094 (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.10117.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.2e-184  600.5   0.0   1.4e-184  600.3   0.0    1.0  1  lcl|MicrobesOnline__882:206529  DVU1094 argininosuccinate lyase


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206529  DVU1094 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.3   0.0  1.4e-184  1.4e-184       1     452 [.       6     456 ..       6     459 .. 0.99

  Alignments for each domain:
  == domain 1  score: 600.3 bits;  conditional E-value: 1.4e-184
                       TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelevdae 79 
                                     +wggR+k+++   v+e+++s+s+D  l+++Di gs+ah+++La++g+lt+eea+ ++++L+++++e+++g++ ++ + e
  lcl|MicrobesOnline__882:206529   6 MWGGRFKQGTATLVEEYTESVSYDRALYAQDIAGSMAHARMLARQGVLTAEEAAIIVDGLATVRSEIEAGSFVWRREFE 84 
                                     6****************************************************************************** PP

                       TIGR00838  80 DiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgytHLqrA 158
                                     D+H+++E++l++ vg dvgkklhtgrsRnDqva d+rl++ d+v+  +e  +dl+ ++v++A++++ tl+pg tH+q A
  lcl|MicrobesOnline__882:206529  85 DVHMNIENRLTELVG-DVGKKLHTGRSRNDQVALDFRLFVSDRVRVWRELGRDLVGVIVDQARQHTATLLPGCTHMQPA 162
                                     ***************.*************************************************************** PP

                       TIGR00838 159 qPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdRDfiiEll 237
                                     qP++la hllaya+ml+rD++Rl d  kR+ ++PlG++Alagt++++d+ ++a+ Lg     +ns+davsdRDf++E+l
  lcl|MicrobesOnline__882:206529 163 QPVSLAQHLLAYAWMLRRDIDRLEDCDKRARVCPLGAAALAGTTYPLDPASVADELGMYGTFRNSMDAVSDRDFVLEAL 241
                                     ******************************************************************************* PP

                       TIGR00838 238 saaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltglltilKalPlaYn 316
                                     ++ +++m+hlsrl+Ee+il++   fg++ l+d++++gssimPqKKnpDvaEl+Rgktgrv+G lt++lt++K+lP++Yn
  lcl|MicrobesOnline__882:206529 242 FDGSVIMAHLSRLCEEFILWANPAFGYIFLPDAYATGSSIMPQKKNPDVAELMRGKTGRVYGALTTMLTTVKGLPMTYN 320
                                     ******************************************************************************* PP

                       TIGR00838 317 kDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaie 395
                                     +DlqEdke++ da +tv+ +le+++g+l+e+++n+ r++ a +++f +at+lAdylv kG+PFReah+++G++va a+e
  lcl|MicrobesOnline__882:206529 321 RDLQEDKEPFIDADRTVSASLEIMAGMLREVRFNTARMRTALRSGFLNATELADYLVGKGIPFREAHHLTGAAVALAEE 399
                                     ******************************************************************************* PP

                       TIGR00838 396 kGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieeaka 452
                                     kG++leel+le ++ +  +++edv+ +l++e av++r++ GGt++++v+ +i+e+ +
  lcl|MicrobesOnline__882:206529 400 KGVTLEELPLEDYRGICDRIDEDVYPILEPEAAVSRRETPGGTGPRSVAAQIAELDS 456
                                     ****************************************************99866 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.23
//
[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