Alignments for a candidate for argH in Oleispira antarctica RB-8

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Oleispira antarctica RB-8

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate WP_046010507.1 OLEAN_RS18780 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>NCBI__GCF_000967895.1:WP_046010507.1
          Length = 463

 Score =  449 bits (1154), Expect = e-130
 Identities = 228/456 (50%), Positives = 309/456 (67%), Gaps = 1/456 (0%)

Query: 6   TWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLVAGL 65
           +W  RF       +AR+ AS+ FD  L  +D+ GS AHAKML   G+++  E + ++ GL
Sbjct: 8   SWGGRFSEPTDAFVARYTASVDFDQRLYAHDIQGSIAHAKMLTKVGVLTQAECDDILRGL 67

Query: 66  EQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLYLRD 125
           E++R E  +G F   ++ EDVH  +E  LT  +G  GKKLHT RSRNDQV TD RLYLRD
Sbjct: 68  EEVRIEIERGDFKWSIELEDVHMNIEAALTAKIGITGKKLHTGRSRNDQVATDIRLYLRD 127

Query: 126 QIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDWERL 185
           +I  I +EL   Q  L+ +A  H +T++PG+THLQ AQPV+  HH+LA+ +M +RD++RL
Sbjct: 128 EIDNIGTELTRLQEGLVGLAAAHSDTIMPGFTHLQTAQPVTFGHHILAWNEMLERDYDRL 187

Query: 186 GDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLCAAS 245
            DV +R+N  PLG  ALAGTT+PIDRHYTA+LL F     NSLD VSDRDFAIEF  A +
Sbjct: 188 LDVRKRLNHLPLGAAALAGTTYPIDRHYTAELLGFTAPTENSLDSVSDRDFAIEFTAAGA 247

Query: 246 LIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVFGHL 305
           +IM+H+SR +EE++LW+S +F+F+ L D   TGSSIMPQKKNPDVPELVRGK+GRV+GHL
Sbjct: 248 IIMMHMSRFSEELVLWASAQFQFIHLPDRFCTGSSIMPQKKNPDVPELVRGKSGRVYGHL 307

Query: 306 QAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQAVTE 365
            ++L +MK  PLAYNKD QEDKE LFD+V+T++ S+ A    +   LE     + +A   
Sbjct: 308 MSLLTLMKSQPLAYNKDNQEDKEPLFDTVDTLRDSIRAFAD-MAPYLEPNKPSMYEAARR 366

Query: 366 DFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAADIY 425
            FS ATD+ADY+  +G+PFR+A+ +VGK V   I  GK L ++ LEE Q+      AD++
Sbjct: 367 GFSTATDLADYVVVKGIPFRDAHEIVGKAVAYGIETGKDLSEMTLEELQKFSDQITADVF 426

Query: 426 EAISPRQVVAARNSHGGTGFVQVSKALIAARAQIDQ 461
           + ++    VAAR+  GGT   QV  A   A  ++ +
Sbjct: 427 DVLTLEGSVAARDHIGGTAPKQVIAAAKRASERLSK 462


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: 565
Number of extensions: 23
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: 463
Length adjustment: 33
Effective length of query: 428
Effective length of database: 430
Effective search space:   184040
Effective search space used:   184040
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 WP_046010507.1 OLEAN_RS18780 (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.1579915.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-196  639.6   0.0   1.9e-196  639.4   0.0    1.0  1  NCBI__GCF_000967895.1:WP_046010507.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000967895.1:WP_046010507.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  639.4   0.0  1.9e-196  1.9e-196       2     454 ..       9     460 ..       8     461 .. 0.99

  Alignments for each domain:
  == domain 1  score: 639.4 bits;  conditional E-value: 1.9e-196
                             TIGR00838   2 wggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklel 74 
                                           wggR+++ +d  va+++as++fD++l+++Di+gsiah+k+L+k+g+lt+ e +++ ++Lee++ e+++g++++
  NCBI__GCF_000967895.1:WP_046010507.1   9 WGGRFSEPTDAFVARYTASVDFDQRLYAHDIQGSIAHAKMLTKVGVLTQAECDDILRGLEEVRIEIERGDFKW 81 
                                           9************************************************************************ PP

                             TIGR00838  75 evdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevet 147
                                           + + eD+H+++E+ l++k+g   gkklhtgrsRnDqvatd+rlylrd+++++ ++l  l++ lv +A+++ +t
  NCBI__GCF_000967895.1:WP_046010507.1  82 SIELEDVHMNIEAALTAKIG-ITGKKLHTGRSRNDQVATDIRLYLRDEIDNIGTELTRLQEGLVGLAAAHSDT 153
                                           ********************.999************************************************* PP

                             TIGR00838 148 lmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavv 220
                                           +mpg+tHLq AqP+t++Hh+la+ emlerD++Rlld+ kR+n+ PlG++Alagt+++idr+++aelLgF a +
  NCBI__GCF_000967895.1:WP_046010507.1 154 IMPGFTHLQTAQPVTFGHHILAWNEMLERDYDRLLDVRKRLNHLPLGAAALAGTTYPIDRHYTAELLGFTAPT 226
                                           ************************************************************************* PP

                             TIGR00838 221 ensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgk 293
                                           ensld+vsdRDf+iE+ +a a++m+h+sr++Eel+l++s+ f+f++l+d++++gssimPqKKnpDv El+Rgk
  NCBI__GCF_000967895.1:WP_046010507.1 227 ENSLDSVSDRDFAIEFTAAGAIIMMHMSRFSEELVLWASAQFQFIHLPDRFCTGSSIMPQKKNPDVPELVRGK 299
                                           ************************************************************************* PP

                             TIGR00838 294 tgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalat 366
                                           +grv+G+l++llt++K++PlaYnkD qEdke+lfd+++t+++++++++ +   l+ nk  + eaa+++f++at
  NCBI__GCF_000967895.1:WP_046010507.1 300 SGRVYGHLMSLLTLMKSQPLAYNKDNQEDKEPLFDTVDTLRDSIRAFADMAPYLEPNKPSMYEAARRGFSTAT 372
                                           ************************************************************************* PP

                             TIGR00838 367 dlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGta 439
                                           dlAdy+v kG+PFR+aheivG++va+ ie+Gk+l+e+tleelqk+s +++ dv++vl+le +v++rd +GGta
  NCBI__GCF_000967895.1:WP_046010507.1 373 DLADYVVVKGIPFRDAHEIVGKAVAYGIETGKDLSEMTLEELQKFSDQITADVFDVLTLEGSVAARDHIGGTA 445
                                           ************************************************************************* PP

                             TIGR00838 440 keevekaieeakael 454
                                           +++v  a + a ++l
  NCBI__GCF_000967895.1:WP_046010507.1 446 PKQVIAAAKRASERL 460
                                           ****99999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (463 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: 15.69
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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