Aligments for a candidate for argH in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Aligments for a candidate for argH in Pseudomonas stutzeri RCH2

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate GFF3683 Psest_3751 argininosuccinate lyase

Query= BRENDA::Q9LAE5
         (461 letters)



>FitnessBrowser__psRCH2:GFF3683
          Length = 464

 Score =  450 bits (1157), Expect = e-131
 Identities = 231/448 (51%), Positives = 306/448 (68%), Gaps = 1/448 (0%)

Query: 5   QTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLVAG 64
           Q+W  RF   +   +ARF AS+ FD  L  +D+ GS AHA ML   G++S++E +Q++A 
Sbjct: 8   QSWGGRFSEPVDAFVARFTASVEFDKRLYRHDIMGSIAHATMLEKAGVLSADERDQIIAN 67

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

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

Query: 185 LGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLCAA 244
           L D  +R N  PLG  ALAGTT+PI R  T +LL F+ I  NSLDGVSDRDFAIEF  AA
Sbjct: 188 LVDCRKRTNRMPLGSAALAGTTYPIQREITCELLGFEAISGNSLDGVSDRDFAIEFCAAA 247

Query: 245 SLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVFGH 304
           SL M+HLSR +EE++LW+S +F+F+ L D   TGSSIMPQKKNPDVPELVRGKTGRVFG 
Sbjct: 248 SLAMMHLSRFSEELVLWTSAQFQFIDLPDRFCTGSSIMPQKKNPDVPELVRGKTGRVFGA 307

Query: 305 LQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQAVT 364
           L  +LV+MKG PLAYNKD QEDKE LFD+ +T++ SL A   ++   ++ + + + +A  
Sbjct: 308 LAGLLVLMKGQPLAYNKDNQEDKEPLFDAADTLRDSLRAFADMV-PAIKPKREIMREAAL 366

Query: 365 EDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAADI 424
             FS ATD+ADYL  +G+PFR+ + +VG  VK  +  GK L ++ L+E +Q     + D+
Sbjct: 367 RGFSTATDLADYLVRKGLPFRDCHEIVGHAVKYGVQTGKDLAEMSLDELRQFSDQISDDV 426

Query: 425 YEAISPRQVVAARNSHGGTGFVQVSKAL 452
           +  ++    V AR+  GGT   QV  A+
Sbjct: 427 FAVLTLEGSVNARDHIGGTAPAQVRAAV 454


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: 515
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 GFF3683 Psest_3751 (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.9972.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     5e-197  641.3   0.0   5.7e-197  641.1   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3683  Psest_3751 argininosuccinate lya


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3683  Psest_3751 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  641.1   0.0  5.7e-197  5.7e-197       2     452 ..      10     459 ..       9     462 .. 0.99

  Alignments for each domain:
  == domain 1  score: 641.1 bits;  conditional E-value: 5.7e-197
                           TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelev 76 
                                         wggR+++ +d  va+f+as++fDk+l+++Di gsiah+++L+kag+l+++e++++i++L++++ e+++g+++++v
  lcl|FitnessBrowser__psRCH2:GFF3683  10 WGGRFSEPVDAFVARFTASVEFDKRLYRHDIMGSIAHATMLEKAGVLSADERDQIIANLKDIQGEIEAGTFDWRV 84 
                                         9************************************************************************** PP

                           TIGR00838  77 daeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpg 151
                                         d eD+H+++E++l+d++g   gkklhtgrsRnDqvatd+rl+lrd+++ ++ ++  l++ l+ +Ae+e +t+mpg
  lcl|FitnessBrowser__psRCH2:GFF3683  85 DLEDVHMNIEARLTDRIG-VTGKKLHTGRSRNDQVATDIRLWLRDEIDIILAEITRLQQGLLGLAEAEADTIMPG 158
                                         ******************.99****************************************************** PP

                           TIGR00838 152 ytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvenslda 226
                                         +tHLq AqP+t++Hhlla++eml+rD+eRl+d  kR+n+ PlGs+Alagt+++i+re + elLgF+a+  nsld+
  lcl|FitnessBrowser__psRCH2:GFF3683 159 FTHLQTAQPVTFGHHLLAWFEMLSRDYERLVDCRKRTNRMPLGSAALAGTTYPIQREITCELLGFEAISGNSLDG 233
                                         *************************************************************************** PP

                           TIGR00838 227 vsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnl 301
                                         vsdRDf+iE+ +aa+l+m+hlsr++Eel+l++s+ f+f++l+d++++gssimPqKKnpDv El+Rgktgrv+G l
  lcl|FitnessBrowser__psRCH2:GFF3683 234 VSDRDFAIEFCAAASLAMMHLSRFSEELVLWTSAQFQFIDLPDRFCTGSSIMPQKKNPDVPELVRGKTGRVFGAL 308
                                         *************************************************************************** PP

                           TIGR00838 302 tglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkG 376
                                         +gll+++K++PlaYnkD qEdke+lfda +t++++l++++ ++  +k ++e ++eaa ++f++atdlAdylvrkG
  lcl|FitnessBrowser__psRCH2:GFF3683 309 AGLLVLMKGQPLAYNKDNQEDKEPLFDAADTLRDSLRAFADMVPAIKPKREIMREAALRGFSTATDLADYLVRKG 383
                                         *************************************************************************** PP

                           TIGR00838 377 vPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieeak 451
                                         +PFR+ heivG++v++ +++Gk+l e++l+el+++s ++++dv+ vl+le +v++rd +GGta+++v+ a++  +
  lcl|FitnessBrowser__psRCH2:GFF3683 384 LPFRDCHEIVGHAVKYGVQTGKDLAEMSLDELRQFSDQISDDVFAVLTLEGSVNARDHIGGTAPAQVRAAVKRGQ 458
                                         **********************************************************************99876 PP

                           TIGR00838 452 a 452
                                         +
  lcl|FitnessBrowser__psRCH2:GFF3683 459 E 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.74
//
[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