Alignments for a candidate for argH in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Shewanella loihica PV-4

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate 5207684 Shew_0206 argininosuccinate lyase (RefSeq)

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



>FitnessBrowser__PV4:5207684
          Length = 453

 Score =  602 bits (1551), Expect = e-176
 Identities = 308/450 (68%), Positives = 352/450 (78%)

Query: 1   MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEE 60
           MALWGGRF+Q +   FK FNDSL  DYRL E+DIVGS+AW+ A+  VG+L+ +E   L++
Sbjct: 1   MALWGGRFSQESSALFKLFNDSLPVDYRLVEEDIVGSIAWADAITGVGILSQQECQSLKQ 60

Query: 61  ALNVLLEDVRARPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLW 120
           AL  LL +V+ +P+ IL S AED HS+VE  LI KVG LGKKLHTGRSRNDQVATDLKLW
Sbjct: 61  ALQELLAEVKDQPETILASGAEDTHSFVEQALIAKVGDLGKKLHTGRSRNDQVATDLKLW 120

Query: 121 CKDTVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDE 180
           CK     LL    QL++AL+  A+   DAVMPGYTHLQRAQPV F HWCLAYVEM  RD 
Sbjct: 121 CKKEGKALLELLAQLKAALLSLAERELDAVMPGYTHLQRAQPVAFGHWCLAYVEMFERDI 180

Query: 181 SRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLS 240
           SRLQD L+RLD  PLG GALAGTAY +DR  LA  LGFAS T NSLDSVSDRDHV+EL S
Sbjct: 181 SRLQDCLQRLDTCPLGTGALAGTAYPMDRYALAKSLGFASPTLNSLDSVSDRDHVIELCS 240

Query: 241 AAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ 300
            AAI M+HLSR AEDLIFFN+GEAGF+EL D+VTSGSSLMPQKKNPDALELIRGK GRV 
Sbjct: 241 DAAISMMHLSRMAEDLIFFNSGEAGFIELDDQVTSGSSLMPQKKNPDALELIRGKTGRVY 300

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

Query: 361 QQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIRQGKPLEDLPLSELQKFSQVIDED 420
           QQGYANATELADYLVAKG+PFREAHH+VGE VVEAI Q KP+E+  L+ LQ F+ VI ED
Sbjct: 361 QQGYANATELADYLVAKGMPFREAHHVVGEVVVEAIAQKKPIEEFELASLQVFASVIQED 420

Query: 421 VYPILSLQSCLDKRAAKGGVSPQQVAQAIA 450
           VY  L++ SCL KR A GG S  QV  A+A
Sbjct: 421 VYQCLTIDSCLAKREALGGTSLTQVKAALA 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: 570
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: 453
Length adjustment: 33
Effective length of query: 424
Effective length of database: 420
Effective search space:   178080
Effective search space used:   178080
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 5207684 Shew_0206 (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.28844.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   3.1e-191  622.2   0.0   3.7e-191  621.9   0.0    1.0  1  lcl|FitnessBrowser__PV4:5207684  Shew_0206 argininosuccinate lyas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5207684  Shew_0206 argininosuccinate lyase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  621.9   0.0  3.7e-191  3.7e-191       1     448 [.       3     450 ..       3     452 .. 0.99

  Alignments for each domain:
  == domain 1  score: 621.9 bits;  conditional E-value: 3.7e-191
                        TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkeg.klelevd 77 
                                      lwggR+++e +  ++ fn+sl  D++l+e+Di gsia++ a++ +gil+++e + l++aL+el  evk++ +  l + 
  lcl|FitnessBrowser__PV4:5207684   3 LWGGRFSQESSALFKLFNDSLPVDYRLVEEDIVGSIAWADAITGVGILSQQECQSLKQALQELLAEVKDQpETILASG 80 
                                      7*******************************************************************9989999*** PP

                        TIGR00838  78 aeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgytHL 155
                                      aeD H+ vE+ li+kvg d+gkklhtgrsRnDqvatdl+l+++++ k l+e l +l++al+ +Ae+e +++mpgytHL
  lcl|FitnessBrowser__PV4:5207684  81 AEDTHSFVEQALIAKVG-DLGKKLHTGRSRNDQVATDLKLWCKKEGKALLELLAQLKAALLSLAERELDAVMPGYTHL 157
                                      *****************.************************************************************ PP

                        TIGR00838 156 qrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdRDfi 233
                                      qrAqP+ ++H++lay+em+erD++Rl+d l+R++++PlG+gAlagt++++dr +la+ LgF++ + nsld+vsdRD++
  lcl|FitnessBrowser__PV4:5207684 158 QRAQPVAFGHWCLAYVEMFERDISRLQDCLQRLDTCPLGTGALAGTAYPMDRYALAKSLGFASPTLNSLDSVSDRDHV 235
                                      ****************************************************************************** PP

                        TIGR00838 234 iEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltglltilKal 311
                                      iEl s+aa+ m+hlsr+aE+li+f+s E+gf+el+d+v+sgss+mPqKKnpD++EliRgktgrv+G+l+g+lt++Kal
  lcl|FitnessBrowser__PV4:5207684 236 IELCSDAAISMMHLSRMAEDLIFFNSGEAGFIELDDQVTSGSSLMPQKKNPDALELIRGKTGRVYGSLMGILTTMKAL 313
                                      ****************************************************************************** PP

                        TIGR00838 312 PlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGev 389
                                      PlaYnkD+qEdke+lfd ++ ++ +le+++++l+ lkvn+e++  aa++++a+at+lAdylv+kG+PFReah++vGev
  lcl|FitnessBrowser__PV4:5207684 314 PLAYNKDMQEDKEGLFDVMDSWSICLEMAALVLSGLKVNRENTLSAAQQGYANATELADYLVAKGMPFREAHHVVGEV 391
                                      ****************************************************************************** PP

                        TIGR00838 390 vakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaie 448
                                      v++ai++ k +ee  l+ lq + + ++edv++ l++ ++++kr+a GGt+ ++v+ a++
  lcl|FitnessBrowser__PV4:5207684 392 VVEAIAQKKPIEEFELASLQVFASVIQEDVYQCLTIDSCLAKREALGGTSLTQVKAALA 450
                                      *******************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (453 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: 10.48
//
[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