Alignments for a candidate for argH in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Pseudomonas fluorescens GW456-L13

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate PfGW456L13_854 Argininosuccinate lyase (EC 4.3.2.1)

Query= SwissProt::Q9LAE5
         (461 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_854
          Length = 464

 Score =  450 bits (1157), Expect = e-131
 Identities = 230/453 (50%), Positives = 306/453 (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  I+ E   G+F   +D EDVH  +E RLT+ +G  GKKLHT RSRNDQV TD RL+LR
Sbjct: 68  LNTIQGEIEAGQFDWRIDLEDVHMNIEARLTDRIGVTGKKLHTGRSRNDQVATDIRLWLR 127

Query: 125 DQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDWER 184
           D+I  I +E+   Q  LL+ AE+   +++PG+THLQ AQPV+  HH+LA+F+M  RD+ER
Sbjct: 128 DEIDLILAEITRLQKGLLEQAEREAASIMPGFTHLQTAQPVTFGHHMLAWFEMLSRDYER 187

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

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

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

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

Query: 425 YEAISPRQVVAARNSHGGTGFVQVSKALIAARA 457
           +  ++    V ARN  GGT   QV  A+   +A
Sbjct: 427 FAVLTLEGSVNARNHIGGTAPAQVKAAVARGQA 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: 516
Number of extensions: 19
Number of successful extensions: 3
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 PfGW456L13_854 (Argininosuccinate lyase (EC 4.3.2.1))
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.23744.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
   2.4e-197  642.4   0.0   2.7e-197  642.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_854  Argininosuccinate lyase (EC 4.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_854  Argininosuccinate lyase (EC 4.3.2.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  642.2   0.0  2.7e-197  2.7e-197       2     452 ..      10     459 ..       9     462 .. 0.99

  Alignments for each domain:
  == domain 1  score: 642.2 bits;  conditional E-value: 2.7e-197
                                              TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakkli 57 
                                                            wggR+++ +d  va+f+as++fD++l+++Di gsiah+++Lak+g+lt+ e++ +i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_854  10 WGGRFSEPVDAFVARFTASVTFDQRLYRHDIMGSIAHATMLAKVGVLTDAERDSII 65 
                                                            9******************************************************* PP

                                              TIGR00838  58 eaLeelkeevkegklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvat 113
                                                            ++L++++ e+++g+++++ d eD+H+++E++l+d++g   gkklhtgrsRnDqvat
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_854  66 DGLNTIQGEIEAGQFDWRIDLEDVHMNIEARLTDRIG-VTGKKLHTGRSRNDQVAT 120
                                                            *************************************.99**************** PP

                                              TIGR00838 114 dlrlylrdkvkelaealkdllkalvekAekevetlmpgytHLqrAqPitlaHhlla 169
                                                            d+rl+lrd+++ ++ ++  l+k l+e+Ae+e   +mpg+tHLq AqP+t++Hh+la
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_854 121 DIRLWLRDEIDLILAEITRLQKGLLEQAEREAASIMPGFTHLQTAQPVTFGHHMLA 176
                                                            ******************************************************** PP

                                              TIGR00838 170 yaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensld 225
                                                            ++eml+rD+eRl+d  kR+n+ PlGs+Alagt+++idre++a+lLgFdav  nsld
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_854 177 WFEMLSRDYERLVDCRKRTNRMPLGSAALAGTTYPIDREYTAQLLGFDAVGGNSLD 232
                                                            ******************************************************** PP

                                              TIGR00838 226 avsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqK 281
                                                             vsdRDf+iE+ saa+++m+hlsr++Eel+l++s+ f+f++l+d++++gssimPqK
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_854 233 NVSDRDFAIEFCSAASIAMMHLSRFSEELVLWTSAQFQFIDLPDRFCTGSSIMPQK 288
                                                            ******************************************************** PP

                                              TIGR00838 282 KnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveell 337
                                                            KnpDv El+Rgktgrv+G l+gllt++K++PlaYnkD qEdke+lfda +t++++l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_854 289 KNPDVPELVRGKTGRVFGALMGLLTLMKGQPLAYNKDNQEDKEPLFDAADTLRDSL 344
                                                            ******************************************************** PP

                                              TIGR00838 338 evvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvaka 393
                                                            ++++ ++  +k ++  ++eaa ++f++atdlAdylvr+G+PFR+ heivG++v++ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_854 345 RAFADMVPAIKPKHAMMREAALRGFSTATDLADYLVRRGLPFRDCHEIVGHAVKYG 400
                                                            ******************************************************** PP

                                              TIGR00838 394 iekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaiee 449
                                                            +++Gk+l e++leel+k+s ++++dv+ vl+le +v++r+ +GGta+++v+ a++ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_854 401 VDSGKDLAEMSLEELRKFSDQIDQDVFAVLTLEGSVNARNHIGGTAPAQVKAAVAR 456
                                                            *****************************************************987 PP

                                              TIGR00838 450 aka 452
                                                             +a
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_854 457 GQA 459
                                                            665 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: 10.90
//
[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