GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argH in Pseudomonas simiae WCS417

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate GFF5380 PS417_27540 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>FitnessBrowser__WCS417:GFF5380
          Length = 464

 Score =  455 bits (1171), Expect = e-132
 Identities = 235/453 (51%), Positives = 305/453 (67%), Gaps = 1/453 (0%)

Query: 5   QTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLVAG 64
           Q+W  RF   +   +ARF AS+ FD  L  +D+ GS AHA MLA  G+++  E + ++ G
Sbjct: 8   QSWGGRFSEPVDAFVARFTASVTFDQRLYRHDIMGSIAHATMLAKVGVLTDAERDSIIDG 67

Query: 65  LEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLYLR 124
           L  IR E   G F   VD EDVH  +E RLT+ +G  GKKLHT RSRNDQV TD RL+LR
Sbjct: 68  LTTIRGEIEAGTFDWRVDLEDVHMNIEARLTDRIGVTGKKLHTGRSRNDQVATDIRLWLR 127

Query: 125 DQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDWER 184
           D+I  I  E+   Q  LL+ AE+  +T++PG+THLQ AQPV+  HHLLA+F+M  RD+ER
Sbjct: 128 DEIDLILGEITRLQKGLLEQAERESDTIMPGFTHLQTAQPVTFGHHLLAWFEMLSRDYER 187

Query: 185 LGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLCAA 244
           L D  +R N  PLG  ALAGTT+PIDR YTA+LL FD +  NSLDGVSDRDFAIEF  AA
Sbjct: 188 LVDCRKRANRMPLGSAALAGTTYPIDREYTAQLLGFDAVGGNSLDGVSDRDFAIEFCAAA 247

Query: 245 SLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVFGH 304
           S+ M+HLSR +EE++LW+S +F+F+ L D   TGSSIMPQKKNPDVPELVRGK+GRVFG 
Sbjct: 248 SIAMMHLSRFSEELVLWTSAQFQFIDLPDRFCTGSSIMPQKKNPDVPELVRGKSGRVFGA 307

Query: 305 LQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQAVT 364
           L  +L +MKG PLAYNKD QEDKE LFD+ +T++ SL A   ++   ++ +   + +A  
Sbjct: 308 LMGLLTLMKGQPLAYNKDNQEDKEPLFDAADTLRDSLRAFADMI-PAIKPKHAIMREAAL 366

Query: 365 EDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAADI 424
             FS ATD+ADYL  RG+PFR+ + +VG  VK  +  GK L ++ LEE +Q       D+
Sbjct: 367 RGFSTATDLADYLVRRGLPFRDCHEIVGHAVKYGVDTGKDLAEMSLEELRQFSDQIEQDV 426

Query: 425 YEAISPRQVVAARNSHGGTGFVQVSKALIAARA 457
           +  ++    V ARN  GGT   QV  A+   +A
Sbjct: 427 FAVLTLEGSVNARNHVGGTAPAQVKAAVARGQA 459


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: 530
Number of extensions: 18
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: 464
Length adjustment: 33
Effective length of query: 428
Effective length of database: 431
Effective search space:   184468
Effective search space used:   184468
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 GFF5380 PS417_27540 (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.1305.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.8e-198  644.7   0.0   5.4e-198  644.5   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF5380  PS417_27540 argininosuccinate ly


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF5380  PS417_27540 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  644.5   0.0  5.4e-198  5.4e-198       2     452 ..      10     459 ..       9     462 .. 0.99

  Alignments for each domain:
  == domain 1  score: 644.5 bits;  conditional E-value: 5.4e-198
                           TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelev 76 
                                         wggR+++ +d  va+f+as++fD++l+++Di gsiah+++Lak+g+lt+ e++ +i++L++++ e+++g+++++v
  lcl|FitnessBrowser__WCS417:GFF5380  10 WGGRFSEPVDAFVARFTASVTFDQRLYRHDIMGSIAHATMLAKVGVLTDAERDSIIDGLTTIRGEIEAGTFDWRV 84 
                                         9************************************************************************** PP

                           TIGR00838  77 daeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpg 151
                                         d eD+H+++E++l+d++g   gkklhtgrsRnDqvatd+rl+lrd+++ ++ ++  l+k l+e+Ae+e +t+mpg
  lcl|FitnessBrowser__WCS417:GFF5380  85 DLEDVHMNIEARLTDRIG-VTGKKLHTGRSRNDQVATDIRLWLRDEIDLILGEITRLQKGLLEQAERESDTIMPG 158
                                         ******************.99****************************************************** PP

                           TIGR00838 152 ytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvenslda 226
                                         +tHLq AqP+t++Hhlla++eml+rD+eRl+d  kR+n+ PlGs+Alagt+++idre++a+lLgFdav  nsld+
  lcl|FitnessBrowser__WCS417:GFF5380 159 FTHLQTAQPVTFGHHLLAWFEMLSRDYERLVDCRKRANRMPLGSAALAGTTYPIDREYTAQLLGFDAVGGNSLDG 233
                                         *************************************************************************** PP

                           TIGR00838 227 vsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnl 301
                                         vsdRDf+iE+ +aa+++m+hlsr++Eel+l++s+ f+f++l+d++++gssimPqKKnpDv El+Rgk+grv+G l
  lcl|FitnessBrowser__WCS417:GFF5380 234 VSDRDFAIEFCAAASIAMMHLSRFSEELVLWTSAQFQFIDLPDRFCTGSSIMPQKKNPDVPELVRGKSGRVFGAL 308
                                         *************************************************************************** PP

                           TIGR00838 302 tglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkG 376
                                         +gllt++K++PlaYnkD qEdke+lfda +t++++l++++ ++  +k ++  ++eaa ++f++atdlAdylvr+G
  lcl|FitnessBrowser__WCS417:GFF5380 309 MGLLTLMKGQPLAYNKDNQEDKEPLFDAADTLRDSLRAFADMIPAIKPKHAIMREAALRGFSTATDLADYLVRRG 383
                                         *************************************************************************** PP

                           TIGR00838 377 vPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieeak 451
                                         +PFR+ heivG++v++ +++Gk+l e++leel+++s ++e+dv+ vl+le +v++r+  GGta+++v+ a++  +
  lcl|FitnessBrowser__WCS417:GFF5380 384 LPFRDCHEIVGHAVKYGVDTGKDLAEMSLEELRQFSDQIEQDVFAVLTLEGSVNARNHVGGTAPAQVKAAVARGQ 458
                                         **********************************************************************98766 PP

                           TIGR00838 452 a 452
                                         a
  lcl|FitnessBrowser__WCS417:GFF5380 459 A 459
                                         5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (464 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: 00:00:00.04
# Mc/sec: 4.62
//
[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:

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