Alignments for a candidate for argH in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Shewanella oneidensis MR-1

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate 199474 SO0279 argininosuccinate lyase (NCBI ptt file)

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



>FitnessBrowser__MR1:199474
          Length = 455

 Score =  590 bits (1522), Expect = e-173
 Identities = 302/454 (66%), Positives = 353/454 (77%)

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 CQSEGAALVARLQTLRSELIALAEREFDAVMPGYTHLQRAQPVTFGHWCLAYVEMIERDF 180

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

Query: 241 AAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ 300
            A+I M+HLSR AEDLIFFNTGEAGF+ LSD VTSGSSLMPQKKNPDALELIRGK GRV 
Sbjct: 241 TASISMMHLSRMAEDLIFFNTGEAGFISLSDEVTSGSSLMPQKKNPDALELIRGKTGRVY 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 VYPILSLQSCLDKRAAKGGVSPQQVAQAIAFAQA 454
           VYP L++++CL KR   GG +  QV QAIA  +A
Sbjct: 421 VYPNLTIEACLAKRDVLGGTALTQVKQAIAAKKA 454


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: 555
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 199474 SO0279 (argininosuccinate lyase (NCBI ptt file))
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.18682.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.4e-189  616.8   0.0   1.5e-189  616.6   0.0    1.0  1  lcl|FitnessBrowser__MR1:199474  SO0279 argininosuccinate lyase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199474  SO0279 argininosuccinate lyase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  616.6   0.0  1.5e-189  1.5e-189       1     452 [.       3     454 ..       3     455 .] 0.99

  Alignments for each domain:
  == domain 1  score: 616.6 bits;  conditional E-value: 1.5e-189
                       TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkeg.klelevda 78 
                                     lwggR+++e++  ++ fn+sl  D++l+e+D+ gsia++ a+a +gi+t++e ++l++aL+el  evk + ++ l + a
  lcl|FitnessBrowser__MR1:199474   3 LWGGRFQGETSALFKLFNDSLPVDYRLFEQDVVGSIAWADAIASVGIITATECSDLKKALNELLVEVKGDpAIILASGA 81 
                                     7*******************************************************************99789999*** PP

                       TIGR00838  79 eDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgytHLqr 157
                                     eDiH+ vE+ li+kvg d+gkklhtgrsRnDqvatdl+l+++ +   l+ +l+ l+++l+ +Ae+e +++mpgytHLqr
  lcl|FitnessBrowser__MR1:199474  82 EDIHSFVESALIAKVG-DLGKKLHTGRSRNDQVATDLKLWCQSEGAALVARLQTLRSELIALAEREFDAVMPGYTHLQR 159
                                     ****************.************************************************************** PP

                       TIGR00838 158 AqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdRDfiiEl 236
                                     AqP+t++H++lay+em+erD++Rl+dalkR+n++PlGsgAlagt++++dr++la  L F++ + nsld+vsdRD+++El
  lcl|FitnessBrowser__MR1:199474 160 AQPVTFGHWCLAYVEMIERDFSRLTDALKRANTCPLGSGALAGTAYQMDRHALALALNFASPTLNSLDSVSDRDHVVEL 238
                                     ******************************************************************************* PP

                       TIGR00838 237 lsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltglltilKalPlaY 315
                                      s+a++ m+hlsr+aE+li+f++ E+gf++lsdev+sgss+mPqKKnpD++EliRgktgrv+G+l+g+lt++KalPlaY
  lcl|FitnessBrowser__MR1:199474 239 CSTASISMMHLSRMAEDLIFFNTGEAGFISLSDEVTSGSSLMPQKKNPDALELIRGKTGRVYGSLVGILTTMKALPLAY 317
                                     ******************************************************************************* PP

                       TIGR00838 316 nkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakai 394
                                     nkD+qEdke+lfd ++ +  +l++++++l+ l vn+ ++  aa++++a+at+lAdylv+kG+PFReah++vG +v++ai
  lcl|FitnessBrowser__MR1:199474 318 NKDMQEDKEGLFDVVDSWAICLDMAALVLSGLVVNRPNALLAAQQGYANATELADYLVSKGMPFREAHHVVGVAVVAAI 396
                                     ******************************************************************************* PP

                       TIGR00838 395 ekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieeaka 452
                                     +k + le  tl+e++ +   +e+dv+  l++e +++krd+ GGta ++v++ai++ ka
  lcl|FitnessBrowser__MR1:199474 397 AKKIPLEGFTLAEFKTFADIIEDDVYPNLTIEACLAKRDVLGGTALTQVKQAIAAKKA 454
                                     **99*************************************************99886 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.49
//
[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