Alignments for a candidate for argH in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Herbaspirillum seropedicae SmR1

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate HSERO_RS14685 HSERO_RS14685 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>FitnessBrowser__HerbieS:HSERO_RS14685
          Length = 464

 Score =  442 bits (1137), Expect = e-128
 Identities = 224/458 (48%), Positives = 305/458 (66%), Gaps = 1/458 (0%)

Query: 3   KEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLV 62
           K + WS RF   +   + R+ AS+ FD  + + D+ GS AHA+MLAH GIIS+ +  ++ 
Sbjct: 8   KGEAWSARFSEPVSDLVKRYTASVFFDNRMAQVDIQGSLAHAEMLAHQGIISAADYAEIQ 67

Query: 63  AGLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLY 122
            G+ QI+ E   G+F   +D EDVH  +EKRLTE+VGD GK+LHT RSRNDQV TD RLY
Sbjct: 68  RGMAQIKGEIEAGQFEWLLDLEDVHLNIEKRLTELVGDAGKRLHTGRSRNDQVATDIRLY 127

Query: 123 LRDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDW 182
           +R  +  I   LRE +  LLD+AE+H +T++PG+TH+Q AQP++  HH+LAY +M  RD 
Sbjct: 128 MRGAVDDIIGLLRELRLALLDLAEQHADTILPGFTHMQVAQPITFGHHVLAYVEMFGRDA 187

Query: 183 ERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLC 242
           ER+ D  +R+N  PLG  ALAGTTFPIDR   AK L FD++  NSLD VSDRDFAIEF  
Sbjct: 188 ERMIDARKRINRLPLGAAALAGTTFPIDRLRVAKTLGFDDVCRNSLDAVSDRDFAIEFCA 247

Query: 243 AASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVF 302
            A+L+M H+SR++EE+++W S    F+ + D   TGSSIMPQKKNPDVPEL RGKTGRV 
Sbjct: 248 GAALVMTHISRMSEELVIWMSPRVGFIDIADRFCTGSSIMPQKKNPDVPELARGKTGRVN 307

Query: 303 GHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQA 362
           GHL A+L +MKG PLAYNKD QEDKE LFD+V+T+  +L     + R G+  + + +  A
Sbjct: 308 GHLIALLTLMKGQPLAYNKDNQEDKEPLFDTVDTLTDTLRIFADMAR-GISVKPEAMRAA 366

Query: 363 VTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAA 422
             + ++ ATD+ADYL  +G+PFR+A+  V   V+T +  G  L DL L + +        
Sbjct: 367 ALQGYATATDLADYLVKKGLPFRDAHEAVAHAVRTCVDKGCDLADLSLADLRAFSDLIGE 426

Query: 423 DIYEAISPRQVVAARNSHGGTGFVQVSKALIAARAQID 460
           D++  ++    VAAR+  GGT   QV  A+   R +++
Sbjct: 427 DVFAVLTLEGSVAARDHIGGTAPKQVRAAIAQLRKELN 464


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: 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 HSERO_RS14685 HSERO_RS14685 (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.22641.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.8e-189  616.4   0.0   2.1e-189  616.2   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS14685  HSERO_RS14685 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS14685  HSERO_RS14685 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  616.2   0.0  2.1e-189  2.1e-189       2     454 ..      12     463 ..      11     464 .] 1.00

  Alignments for each domain:
  == domain 1  score: 616.2 bits;  conditional E-value: 2.1e-189
                                  TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 
                                                w+ R+++ +++ v++++as+ fD+++a+ Di+gs+ah+++La++gi+++ + ++++++++++k e+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS14685  12 WSARFSEPVSDLVKRYTASVFFDNRMAQVDIQGSLAHAEMLAHQGIISAADYAEIQRGMAQIKGEIEA 79 
                                                9******************************************************************* PP

                                  TIGR00838  70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkal 137
                                                g++e+  d eD+Hl++E++l++ vg d+gk+lhtgrsRnDqvatd+rly+r +v++++  l++l+ al
  lcl|FitnessBrowser__HerbieS:HSERO_RS14685  80 GQFEWLLDLEDVHLNIEKRLTELVG-DAGKRLHTGRSRNDQVATDIRLYMRGAVDDIIGLLRELRLAL 146
                                                *************************.****************************************** PP

                                  TIGR00838 138 vekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfei 205
                                                +++Ae++ +t++pg+tH+q AqPit++Hh+lay+em+ rD eR++da kR+n+ PlG++Alagt+f+i
  lcl|FitnessBrowser__HerbieS:HSERO_RS14685 147 LDLAEQHADTILPGFTHMQVAQPITFGHHVLAYVEMFGRDAERMIDARKRINRLPLGAAALAGTTFPI 214
                                                ******************************************************************** PP

                                  TIGR00838 206 drellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevss 273
                                                dr ++a++LgFd+v++nsldavsdRDf+iE+ + aal+m+h+sr++Eel+++ s  +gf++++d++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS14685 215 DRLRVAKTLGFDDVCRNSLDAVSDRDFAIEFCAGAALVMTHISRMSEELVIWMSPRVGFIDIADRFCT 282
                                                ******************************************************************** PP

                                  TIGR00838 274 gssimPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvt 341
                                                gssimPqKKnpDv El+Rgktgrv+G+l++llt++K++PlaYnkD qEdke+lfd+++t++++l++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS14685 283 GSSIMPQKKNPDVPELARGKTGRVNGHLIALLTLMKGQPLAYNKDNQEDKEPLFDTVDTLTDTLRIFA 350
                                                ******************************************************************** PP

                                  TIGR00838 342 gllkelkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelq 409
                                                 + + + v+ e ++ aa +++a+atdlAdylv+kG+PFR+ahe v ++v+++++kG +l +l+l+ l+
  lcl|FitnessBrowser__HerbieS:HSERO_RS14685 351 DMARGISVKPEAMRAAALQGYATATDLADYLVKKGLPFRDAHEAVAHAVRTCVDKGCDLADLSLADLR 418
                                                ******************************************************************** PP

                                  TIGR00838 410 klsekleedvlevldleeavekrdakGGtakeevekaieeakael 454
                                                ++s  + edv+ vl+le +v++rd +GGta+++v+ ai+++++el
  lcl|FitnessBrowser__HerbieS:HSERO_RS14685 419 AFSDLIGEDVFAVLTLEGSVAARDHIGGTAPKQVRAAIAQLRKEL 463
                                                ****************************************99987 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: 00:00:00.02
# Mc/sec: 7.82
//
[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