Alignments for a candidate for argH in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Dechlorosoma suillum PS

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate Dsui_0111 Dsui_0111 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>FitnessBrowser__PS:Dsui_0111
          Length = 461

 Score =  452 bits (1163), Expect = e-131
 Identities = 239/454 (52%), Positives = 301/454 (66%), Gaps = 1/454 (0%)

Query: 6   TWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLVAGL 65
           TW+ RF   +   + R+ AS+ FD  L   D+ GS AHA+MLA  GII++ +   +  G+
Sbjct: 9   TWAGRFSEPMSDLVKRYTASVDFDQRLWRQDINGSLAHARMLAKQGIIAAADLADIEKGM 68

Query: 66  EQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLYLRD 125
            QI +E   GKF   +D EDVH  +EKRLT +VGD GK+LHT RSRNDQV TD RL+LRD
Sbjct: 69  AQIVEEIESGKFEWSLDLEDVHLNIEKRLTTLVGDAGKRLHTGRSRNDQVATDIRLWLRD 128

Query: 126 QIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDWERL 185
            I  I   ++ FQ  LL +AEK   T +PG THLQ AQPV+  HHLLAYF+M QRD ER 
Sbjct: 129 TIDSIVELIKAFQTALLVLAEKEAATPMPGSTHLQVAQPVTFGHHLLAYFEMTQRDKERF 188

Query: 186 GDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLCAAS 245
            D  +RVN  PLG  ALAGTT+PIDR + A  L FD +  NSLD VSDRDF IEF  AAS
Sbjct: 189 LDCRKRVNRLPLGAAALAGTTYPIDREFVAAQLGFDGVCENSLDAVSDRDFGIEFCAAAS 248

Query: 246 LIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVFGHL 305
           L+M H SRL+EE++LW +  F +V + D   TGSSIMPQKKNPDVPEL RGKTGRV G L
Sbjct: 249 LLMTHFSRLSEELVLWMNPRFGYVKIADRFCTGSSIMPQKKNPDVPELARGKTGRVNGSL 308

Query: 306 QAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQAVTE 365
            +ML +MKG PLAYNKD QEDKE LFD+ +TV  +L     ++  G+E R +R+  A+ E
Sbjct: 309 ISMLTLMKGQPLAYNKDNQEDKEPLFDAADTVIDTLRIFADMM-GGIEARPERMRGALAE 367

Query: 366 DFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAADIY 425
            F+ ATD+ADYL  +G+PFREA+ +VG  VK +   GK L DL L E Q   P   +D+ 
Sbjct: 368 GFATATDLADYLVKKGLPFREAHEVVGAAVKAAETQGKDLADLTLAELQAFSPLVQSDVA 427

Query: 426 EAISPRQVVAARNSHGGTGFVQVSKALIAARAQI 459
             ++    +AARN  GGT   QV  A+  A+A++
Sbjct: 428 TCLTIEGSLAARNHIGGTAPEQVKAAIARAKARV 461


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: 518
Number of extensions: 13
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: 461
Length adjustment: 33
Effective length of query: 428
Effective length of database: 428
Effective search space:   183184
Effective search space used:   183184
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 Dsui_0111 Dsui_0111 (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.11883.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   4.1e-192  625.1   0.0   4.6e-192  624.9   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_0111  Dsui_0111 argininosuccinate lyas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0111  Dsui_0111 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  624.9   0.0  4.6e-192  4.6e-192       1     453 [.       9     460 ..       9     461 .] 1.00

  Alignments for each domain:
  == domain 1  score: 624.9 bits;  conditional E-value: 4.6e-192
                         TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelevd 77 
                                       +w+gR+++ +++ v++++as++fD++l ++Di+gs+ah+++Lak+gi+ + + ++++++++++ ee+++gk+e++ d
  lcl|FitnessBrowser__PS:Dsui_0111   9 TWAGRFSEPMSDLVKRYTASVDFDQRLWRQDINGSLAHARMLAKQGIIAAADLADIEKGMAQIVEEIESGKFEWSLD 85 
                                       5**************************************************************************** PP

                         TIGR00838  78 aeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgytH 154
                                        eD+Hl++E++l+  vg d+gk+lhtgrsRnDqvatd+rl+lrd++++++e +k++++al+ +Aeke  t mpg tH
  lcl|FitnessBrowser__PS:Dsui_0111  86 LEDVHLNIEKRLTTLVG-DAGKRLHTGRSRNDQVATDIRLWLRDTIDSIVELIKAFQTALLVLAEKEAATPMPGSTH 161
                                       *****************.*********************************************************** PP

                         TIGR00838 155 LqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdRD 231
                                       Lq AqP+t++Hhllay+em +rD eR+ld  kRvn+ PlG++Alagt+++idre++a++LgFd v+ensldavsdRD
  lcl|FitnessBrowser__PS:Dsui_0111 162 LQVAQPVTFGHHLLAYFEMTQRDKERFLDCRKRVNRLPLGAAALAGTTYPIDREFVAAQLGFDGVCENSLDAVSDRD 238
                                       ***************************************************************************** PP

                         TIGR00838 232 fiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltglltil 308
                                       f iE+ +aa+llm+h+srl+Eel+l+    fg+v+++d++++gssimPqKKnpDv El+Rgktgrv+G+l+++lt++
  lcl|FitnessBrowser__PS:Dsui_0111 239 FGIEFCAAASLLMTHFSRLSEELVLWMNPRFGYVKIADRFCTGSSIMPQKKNPDVPELARGKTGRVNGSLISMLTLM 315
                                       ***************************************************************************** PP

                         TIGR00838 309 KalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReahei 385
                                       K++PlaYnkD qEdke+lfda +tv ++l++++ ++  ++ + er++ a +++fa+atdlAdylv+kG+PFReahe+
  lcl|FitnessBrowser__PS:Dsui_0111 316 KGQPLAYNKDNQEDKEPLFDAADTVIDTLRIFADMMGGIEARPERMRGALAEGFATATDLADYLVKKGLPFREAHEV 392
                                       ***************************************************************************** PP

                         TIGR00838 386 vGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieeakae 453
                                       vG++v++a+ +Gk+l +ltl+elq++s+ ++ dv + l++e ++++r+ +GGta+e+v+ ai+ aka+
  lcl|FitnessBrowser__PS:Dsui_0111 393 VGAAVKAAETQGKDLADLTLAELQAFSPLVQSDVATCLTIEGSLAARNHIGGTAPEQVKAAIARAKAR 460
                                       ******************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (461 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: 00:00:00.02
# Mc/sec: 9.44
//
[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