Alignments for a candidate for argG in Halococcus hamelinensis 100A6

GapMind for Amino acid biosynthesis

Alignments for a candidate for argG in Halococcus hamelinensis 100A6

Align Argininosuccinate synthase; EC 6.3.4.5; Citrulline--aspartate ligase (uncharacterized)
to candidate WP_007691434.1 C447_RS04745 argininosuccinate synthase

Query= curated2:Q5UZ46
         (420 letters)



>NCBI__GCF_000336675.1:WP_007691434.1
          Length = 425

 Score =  596 bits (1536), Expect = e-175
 Identities = 289/419 (68%), Positives = 348/419 (83%), Gaps = 1/419 (0%)

Query: 2   PEGNGTVALAFSGGLDTTVCVSLLKEEYGYDEVIGVTVDVGQPDYEFEEAEETAEALGVE 61
           P+    VALAFSGGLDTTVCV +L+EEYGYDEV+GVTVDVGQP  EF EAEETAEAL +E
Sbjct: 7   PDSTDRVALAFSGGLDTTVCVPILEEEYGYDEVVGVTVDVGQPTKEFAEAEETAEALDLE 66

Query: 62  QHVVDATEEFADLCMEAVKANADYQGYPLGTALARPVIAKAILSVAEDEGCSAVAHGCTG 121
            +VVDA + FAD C++AV+ANA YQGYPLGTALARPVIA+AIL VA +  CSA+AHGCTG
Sbjct: 67  HYVVDAKDAFADTCLDAVRANATYQGYPLGTALARPVIAEAILDVALENDCSALAHGCTG 126

Query: 122 KGNDQLRFESVWRDSDLDVIAPVRELGLTREWENEYAAEKGLPVEGGDGGRYSIDTNLWS 181
           KGNDQLRFE+VWRDS+LDVIAPVRELGLTRE E EYA E+ LPVEGG+ G +SIDTNLWS
Sbjct: 127 KGNDQLRFEAVWRDSELDVIAPVRELGLTREVEQEYADERDLPVEGGNAGAWSIDTNLWS 186

Query: 182 RSIEGSELEDPSTIPADDIYKWTDNPSDKDAELVEVEFEDGVPVAVDGEELGGVELIEQL 241
           RS+EGSELE+P+ +P +DIY WT +PS  + EL+E+EFEDG PVA+DGE +  +ELIE+L
Sbjct: 187 RSVEGSELEEPNYVPPEDIYDWTQSPSG-ETELLELEFEDGYPVALDGEAMDPIELIEEL 245

Query: 242 NKQAGAHGIGRTDMMEDRMLGLKVRENYEHPAATVLLTAHEALEGLVLTQEERQFKAQVD 301
           N+ AG+HG+GRTD+MEDRMLGLKVRENYEHPAATVLL AHEALE LVLT+EER FK  +D
Sbjct: 246 NEVAGSHGVGRTDLMEDRMLGLKVRENYEHPAATVLLNAHEALESLVLTKEERSFKKGID 305

Query: 302 QEWSQKAYQGLVDAPLTGALEAFIDDTNERVTGTVTVKLEGGHCRPVSRESDYAVYSESA 361
            EW++KAY+GL+ APL  AL+ FID T ERVTG+VT+KL+GG  R V RES+Y VYS +A
Sbjct: 306 HEWAEKAYEGLLAAPLVDALDGFIDSTQERVTGSVTMKLDGGQARAVGRESEYGVYSAAA 365

Query: 362 ASFNEEDVSGGITQQDATGVAKYHGFQSRLANKILDDAKKGAAVTDGSGDHAASEDTEE 420
           ASFN  DV GGI Q DATGVAKYHGFQSRLA+++++ A+    + DG  +   ++++ E
Sbjct: 366 ASFNTADVGGGIEQADATGVAKYHGFQSRLASRVMESAESAKPLADGGNESDGTDESGE 424


Lambda     K      H
   0.310    0.131    0.374 

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: 706
Number of extensions: 22
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: 420
Length of database: 425
Length adjustment: 32
Effective length of query: 388
Effective length of database: 393
Effective search space:   152484
Effective search space used:   152484
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_007691434.1 C447_RS04745 (argininosuccinate synthase)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))

# 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/TIGR00032.hmm
# target sequence database:        /tmp/gapView.2703195.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00032  [M=394]
Accession:   TIGR00032
Description: argG: argininosuccinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-137  445.0   0.0   1.7e-137  444.8   0.0    1.0  1  NCBI__GCF_000336675.1:WP_007691434.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000336675.1:WP_007691434.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.8   0.0  1.7e-137  1.7e-137       1     393 [.      12     400 ..      12     401 .. 0.97

  Alignments for each domain:
  == domain 1  score: 444.8 bits;  conditional E-value: 1.7e-137
                             TIGR00032   1 kvvlaysGGlDtsvalklleek.ga.eviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfa 71 
                                           +v+la+sGGlDt+v+++ lee+ g+ ev+ vtvdvGqp ++++++ee a +l   ++yv+Da++ f++   + 
  NCBI__GCF_000336675.1:WP_007691434.1  12 RVALAFSGGLDTTVCVPILEEEyGYdEVVGVTVDVGQPTKEFAEAEETAEAL-DLEHYVVDAKDAFADT-CLD 82 
                                           699**********************9************************99.899***********99.*** PP

                             TIGR00032  72 aiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvrel 144
                                           a++ana+y+g Y+l+taLaRp+ia+++++va +++++a+ahGctgKGnDq+RFe++ +  +++l+viaPvrel
  NCBI__GCF_000336675.1:WP_007691434.1  83 AVRANATYQG-YPLGTALARPVIAEAILDVALENDCSALAHGCTGKGNDQLRFEAVWR--DSELDVIAPVREL 152
                                           **********.*********************************************99..99*********** PP

                             TIGR00032 145 eliReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevvei 217
                                            l+Re e eya e+ ++v+  ++ a+siD nl++rs+E++eLE+p+ +ppediy+++++p  +t    e +e+
  NCBI__GCF_000336675.1:WP_007691434.1 153 GLTREVEQEYADERDLPVEGGNAGAWSIDTNLWSRSVEGSELEEPNYVPPEDIYDWTQSPSGET----ELLEL 221
                                           **********************************************************888777....9**** PP

                             TIGR00032 218 eFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvlt 290
                                           eFe+G Pval+ge ++p+eli+++ne+ag hGvGr+D +EdR++glK Re+YE+pa+++L++Ah++Le+lvlt
  NCBI__GCF_000336675.1:WP_007691434.1 222 EFEDGYPVALDGEAMDPIELIEELNEVAGSHGVGRTDLMEDRMLGLKVRENYEHPAATVLLNAHEALESLVLT 294
                                           ************************************************************************* PP

                             TIGR00032 291 kdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvs 363
                                           k+++ fk+ ++++++e  Y+Gl+  pl +ald +i+ tqervtG v++kl  G+a+ +gr+sey +Y++  +s
  NCBI__GCF_000336675.1:WP_007691434.1 295 KEERSFKKGIDHEWAEKAYEGLLAAPLVDALDGFIDSTQERVTGSVTMKLDGGQARAVGRESEYGVYSAAAAS 367
                                           ************************************************************************* PP

                             TIGR00032 364 fek...dkefdqkdaiGfikirglqikvyrekl 393
                                           f+       ++q da+G+ k++g+q +  ++++
  NCBI__GCF_000336675.1:WP_007691434.1 368 FNTadvGGGIEQADATGVAKYHGFQSRLASRVM 400
                                           *98533457****************99888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (425 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: 00:00:00.02
# Mc/sec: 7.84
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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