Aligments for a candidate for argH in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Aligments for a candidate for argH in Pseudomonas fluorescens FW300-N2E2

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate Pf6N2E2_4429 Argininosuccinate lyase (EC 4.3.2.1)

Query= BRENDA::Q9LAE5
         (461 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4429
          Length = 464

 Score =  450 bits (1158), Expect = e-131
 Identities = 229/453 (50%), Positives = 308/453 (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   QSWGGRFSEPVDAFVARFTASVNFDQRLYRHDIMGSIAHATMLAKVGVLTDAERDSIIDG 67

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

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

Query: 185 LGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLCAA 244
           L D  +R N  PLG  ALAGTT+PIDR YTA+LL FD +  NSLD VSDRDFAIEF  AA
Sbjct: 188 LVDCRKRTNRMPLGSAALAGTTYPIDREYTAQLLGFDAVGGNSLDNVSDRDFAIEFCAAA 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-PAIKPKHAVMREAAL 366

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

Query: 425 YEAISPRQVVAARNSHGGTGFVQVSKALIAARA 457
           +  ++    V AR+  GGT   QV  A++  +A
Sbjct: 427 FAVLTLEGSVNARDHIGGTAPAQVKAAVVRGQA 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: 514
Number of extensions: 16
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 Pf6N2E2_4429 (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.21393.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   9.2e-197  640.4   0.0     1e-196  640.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4429  Argininosuccinate lyase (EC 4.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4429  Argininosuccinate lyase (EC 4.3.2.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  640.3   0.0    1e-196    1e-196       2     449 ..      10     456 ..       9     462 .. 0.99

  Alignments for each domain:
  == domain 1  score: 640.3 bits;  conditional E-value: 1e-196
                                      TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelke 65 
                                                    wggR+++ +d  va+f+as++fD++l+++Di gsiah+++Lak+g+lt+ e++ +i++L++++ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4429  10 WGGRFSEPVDAFVARFTASVNFDQRLYRHDIMGSIAHATMLAKVGVLTDAERDSIIDGLKTIQA 73 
                                                    9*************************************************************** PP

                                      TIGR00838  66 evkegklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaea 129
                                                    e+++g+++++vd eD+H+++E++l+d++g   gkklhtgrsRnDqvatd+rl+lrd+++ ++ +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4429  74 EIEAGQFDWRVDLEDVHMNIEARLTDRIG-VTGKKLHTGRSRNDQVATDIRLWLRDEIDLILAE 136
                                                    *****************************.99******************************** PP

                                      TIGR00838 130 lkdllkalvekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPl 193
                                                    +  l+k l+e+A +e e +mpg+tHLq AqP+t++Hh+la++eml+rD+eRl+d  kR+n+ Pl
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4429 137 ITRLQKGLLEQAGREAESIMPGFTHLQTAQPVTFGHHMLAWFEMLSRDYERLVDCRKRTNRMPL 200
                                                    **************************************************************** PP

                                      TIGR00838 194 GsgAlagtsfeidrellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilf 257
                                                    Gs+Alagt+++idre++a+lLgFdav  nsld vsdRDf+iE+ +aa+++m+hlsr++Eel+l+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4429 201 GSAALAGTTYPIDREYTAQLLGFDAVGGNSLDNVSDRDFAIEFCAAASIAMMHLSRFSEELVLW 264
                                                    **************************************************************** PP

                                      TIGR00838 258 sseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqE 321
                                                    +s+ f+f++l+d++++gssimPqKKnpDv El+Rgk+grv+G l+gllt++K++PlaYnkD qE
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4429 265 TSAQFQFIDLPDRFCTGSSIMPQKKNPDVPELVRGKSGRVFGALMGLLTLMKGQPLAYNKDNQE 328
                                                    **************************************************************** PP

                                      TIGR00838 322 dkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReahei 385
                                                    dke+lfda +t++++l++++ ++  +k ++  ++eaa ++f++atdlAdylvr+G+PFR+ hei
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4429 329 DKEPLFDAADTLRDSLRAFADMIPAIKPKHAVMREAALRGFSTATDLADYLVRRGLPFRDCHEI 392
                                                    **************************************************************** PP

                                      TIGR00838 386 vGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaiee 449
                                                    vG++v++ +++Gk+l e++l+el+++s ++e+dv+ vl+le +v++rd +GGta+++v+ a+  
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4429 393 VGHAVKYGVDSGKDLAEMSLDELRQFSDQIEQDVFAVLTLEGSVNARDHIGGTAPAQVKAAVVR 456
                                                    ***********************************************************99865 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.19
//
[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