GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argH in Shewanella sp. ANA-3

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate 7026769 Shewana3_3901 argininosuccinate lyase (RefSeq)

Query= ecocyc::ARGSUCCINLYA-MONOMER
         (457 letters)



>FitnessBrowser__ANA3:7026769
          Length = 455

 Score =  589 bits (1519), Expect = e-173
 Identities = 299/450 (66%), Positives = 351/450 (78%)

Query: 1   MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEE 60
           MALWGGRF       FK FNDSL  DYRL EQD+VGS+AW+ A+ +VG++TA E + L++
Sbjct: 1   MALWGGRFQGETSALFKLFNDSLPVDYRLFEQDVVGSIAWADAIASVGIITATECSDLKK 60

Query: 61  ALNVLLEDVRARPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLW 120
           ALN LL +V+  P  IL S AEDIHS+VE  LI KVG LGKKLHTGRSRNDQVATDLKLW
Sbjct: 61  ALNELLVEVKGDPAIILASGAEDIHSFVESALIAKVGDLGKKLHTGRSRNDQVATDLKLW 120

Query: 121 CKDTVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDE 180
           C+   + L+   + L+S L+  A+   DAVMPGYTHLQRAQPVTF HWCLAYVEM+ RD 
Sbjct: 121 CQSEGAALVARLQTLRSELIALAEREFDAVMPGYTHLQRAQPVTFGHWCLAYVEMIERDL 180

Query: 181 SRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLS 240
           SRL DALKR +  PLG GALAGTAY++DR  LA  L FAS T NSLDSVSDRDHV+EL S
Sbjct: 181 SRLTDALKRANTCPLGSGALAGTAYQMDRHALAAALNFASPTLNSLDSVSDRDHVVELCS 240

Query: 241 AAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ 300
            A+I M+HLSR AEDLIFFN+GEAGF+ LSD VTSGSSLMPQKKNPDALELIRGK GRV 
Sbjct: 241 TASISMIHLSRMAEDLIFFNSGEAGFISLSDEVTSGSSLMPQKKNPDALELIRGKTGRVY 300

Query: 301 GALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCQEAA 360
           G+L G++ T+K LPLAYNKDMQEDKEGLFD +D+W  CL MAALVL G+ V RP    AA
Sbjct: 301 GSLVGILTTMKALPLAYNKDMQEDKEGLFDVVDSWAICLDMAALVLSGLVVNRPNALLAA 360

Query: 361 QQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIRQGKPLEDLPLSELQKFSQVIDED 420
           QQGYANATELADYLV+KG+PFREAHH+VG AVV AI +  PLE   L+E + F+ +I++D
Sbjct: 361 QQGYANATELADYLVSKGMPFREAHHVVGVAVVAAIAKKIPLEGFTLAEFKTFADIIEDD 420

Query: 421 VYPILSLQSCLDKRAAKGGVSPQQVAQAIA 450
           VYP L++++CL KR   GG +  QV QAI+
Sbjct: 421 VYPNLTIEACLAKRDVLGGTALTQVKQAIS 450


Lambda     K      H
   0.318    0.133    0.386 

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: 548
Number of extensions: 15
Number of successful extensions: 1
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: 457
Length of database: 455
Length adjustment: 33
Effective length of query: 424
Effective length of database: 422
Effective search space:   178928
Effective search space used:   178928
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate 7026769 Shewana3_3901 (argininosuccinate lyase (RefSeq))
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.1162477.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.8e-189  615.7   0.0   3.2e-189  615.6   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7026769  Shewana3_3901 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026769  Shewana3_3901 argininosuccinate lyase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  615.6   0.0  3.2e-189  3.2e-189       1     451 [.       3     453 ..       3     455 .] 0.99

  Alignments for each domain:
  == domain 1  score: 615.6 bits;  conditional E-value: 3.2e-189
                         TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkeg.klelev 76 
                                       lwggR+++e++  ++ fn+sl  D++l+e+D+ gsia++ a+a +gi+t++e ++l++aL+el  evk + ++ l +
  lcl|FitnessBrowser__ANA3:7026769   3 LWGGRFQGETSALFKLFNDSLPVDYRLFEQDVVGSIAWADAIASVGIITATECSDLKKALNELLVEVKGDpAIILAS 79 
                                       7*******************************************************************99789999* PP

                         TIGR00838  77 daeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgyt 153
                                        aeDiH+ vE+ li+kvg d+gkklhtgrsRnDqvatdl+l+++ +   l+ +l+ l+++l+ +Ae+e +++mpgyt
  lcl|FitnessBrowser__ANA3:7026769  80 GAEDIHSFVESALIAKVG-DLGKKLHTGRSRNDQVATDLKLWCQSEGAALVARLQTLRSELIALAEREFDAVMPGYT 155
                                       ******************.********************************************************** PP

                         TIGR00838 154 HLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdR 230
                                       HLqrAqP+t++H++lay+em+erDl+Rl+dalkR+n++PlGsgAlagt++++dr++la+ L F++ + nsld+vsdR
  lcl|FitnessBrowser__ANA3:7026769 156 HLQRAQPVTFGHWCLAYVEMIERDLSRLTDALKRANTCPLGSGALAGTAYQMDRHALAAALNFASPTLNSLDSVSDR 232
                                       ***************************************************************************** PP

                         TIGR00838 231 DfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltgllti 307
                                       D+++El s+a++ m+hlsr+aE+li+f+s E+gf++lsdev+sgss+mPqKKnpD++EliRgktgrv+G+l+g+lt+
  lcl|FitnessBrowser__ANA3:7026769 233 DHVVELCSTASISMIHLSRMAEDLIFFNSGEAGFISLSDEVTSGSSLMPQKKNPDALELIRGKTGRVYGSLVGILTT 309
                                       ***************************************************************************** PP

                         TIGR00838 308 lKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReahe 384
                                       +KalPlaYnkD+qEdke+lfd ++ +  +l++++++l+ l vn+ ++  aa++++a+at+lAdylv+kG+PFReah+
  lcl|FitnessBrowser__ANA3:7026769 310 MKALPLAYNKDMQEDKEGLFDVVDSWAICLDMAALVLSGLVVNRPNALLAAQQGYANATELADYLVSKGMPFREAHH 386
                                       ***************************************************************************** PP

                         TIGR00838 385 ivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieeak 451
                                       +vG +v++ai+k + le  tl+e++ +   +e+dv+  l++e +++krd+ GGta ++v++ai++ k
  lcl|FitnessBrowser__ANA3:7026769 387 VVGVAVVAAIAKKIPLEGFTLAEFKTFADIIEDDVYPNLTIEACLAKRDVLGGTALTQVKQAISAKK 453
                                       ************99*************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (455 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 16.96
//
[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