Alignments for a candidate for argH in Thioalkalivibrio denitrificans ALJD

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Thioalkalivibrio denitrificans ALJD

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate WP_077278530.1 B1C78_RS07430 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>NCBI__GCF_002000365.1:WP_077278530.1
          Length = 467

 Score =  471 bits (1211), Expect = e-137
 Identities = 237/458 (51%), Positives = 318/458 (69%), Gaps = 1/458 (0%)

Query: 4   EQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLVA 63
           ++ W  RF  A    +  F AS+ FD  L  +D+ GS+AHA+MLA  G+++ +E  ++  
Sbjct: 8   DKLWGGRFAEATDAFVEAFTASVDFDQRLYRHDIEGSRAHARMLARVGVLTDDECRRIQE 67

Query: 64  GLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLYL 123
           GL+ I  +  +G F    + EDVH  +E RL E +GD GKKLHT RSRNDQV TD RLYL
Sbjct: 68  GLDDILADIERGDFAWLTELEDVHMNIEARLIERIGDTGKKLHTGRSRNDQVATDIRLYL 127

Query: 124 RDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDWE 183
           R+ I  +  E+R  Q  LLD+AE+  +T++PG+THLQ AQPV+  HH++A+F+M +RD  
Sbjct: 128 REAIDALILEIRRLQAGLLDLAEREADTIMPGFTHLQTAQPVTFGHHMMAWFEMLERDHA 187

Query: 184 RLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLCA 243
           RL D  RRVN+ PLG  ALAGT++P+DR YTA+LL FD++  NSLD VSDRDFAIEF  A
Sbjct: 188 RLQDCRRRVNVLPLGAAALAGTSYPLDRRYTAQLLGFDDVTDNSLDSVSDRDFAIEFCAA 247

Query: 244 ASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVFG 303
            +LIM HLSR +EE+ILW+S +F FV L D   TGSSIMPQKKNPDVPELVRGKTGRV G
Sbjct: 248 GALIMTHLSRFSEELILWASAQFGFVDLPDRFCTGSSIMPQKKNPDVPELVRGKTGRVNG 307

Query: 304 HLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQAV 363
           +L A+L +MKG PLAYNKD QEDKE LFD+V+T+  SL A   ++   ++ R + + +A 
Sbjct: 308 NLVALLTLMKGQPLAYNKDNQEDKEPLFDTVDTLAGSLRAFADMVPH-IQVRAETMREAA 366

Query: 364 TEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAAD 423
           +  F+ ATD+ADYL  RG+PFR+A+ +VGK V+  +  G+ L ++ LEE Q       AD
Sbjct: 367 SRGFATATDLADYLVRRGMPFRDAHEVVGKAVRHGVETGRDLGEMRLEELQGFSKMIEAD 426

Query: 424 IYEAISPRQVVAARNSHGGTGFVQVSKALIAARAQIDQ 461
           +++ ++    VAARN HGGT   QV   + AARA++D+
Sbjct: 427 VFDVLTLEGSVAARNVHGGTAPEQVLARIRAARAELDK 464


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: 531
Number of extensions: 14
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: 467
Length adjustment: 33
Effective length of query: 428
Effective length of database: 434
Effective search space:   185752
Effective search space used:   185752
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_077278530.1 B1C78_RS07430 (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.17263.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-201  656.0   0.0   1.9e-201  655.8   0.0    1.0  1  lcl|NCBI__GCF_002000365.1:WP_077278530.1  B1C78_RS07430 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002000365.1:WP_077278530.1  B1C78_RS07430 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  655.8   0.0  1.9e-201  1.9e-201       1     454 [.      10     462 ..      10     463 .. 1.00

  Alignments for each domain:
  == domain 1  score: 655.8 bits;  conditional E-value: 1.9e-201
                                 TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 
                                               lwggR+++++d  v++f+as++fD++l+++Diegs ah+++La++g+lt++e ++++e+L+++  ++++
  lcl|NCBI__GCF_002000365.1:WP_077278530.1  10 LWGGRFAEATDAFVEAFTASVDFDQRLYRHDIEGSRAHARMLARVGVLTDDECRRIQEGLDDILADIER 78 
                                               7******************************************************************** PP

                                 TIGR00838  70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138
                                               g++ + ++ eD+H+++E++li+++g d gkklhtgrsRnDqvatd+rlylr++++ l+ +++ l++ l+
  lcl|NCBI__GCF_002000365.1:WP_077278530.1  79 GDFAWLTELEDVHMNIEARLIERIG-DTGKKLHTGRSRNDQVATDIRLYLREAIDALILEIRRLQAGLL 146
                                               *************************.******************************************* PP

                                 TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207
                                               ++Ae+e +t+mpg+tHLq AqP+t++Hh++a++emlerD  Rl+d  +Rvn+ PlG++Alagts+++dr
  lcl|NCBI__GCF_002000365.1:WP_077278530.1 147 DLAEREADTIMPGFTHLQTAQPVTFGHHMMAWFEMLERDHARLQDCRRRVNVLPLGAAALAGTSYPLDR 215
                                               ********************************************************************* PP

                                 TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276
                                               +++a+lLgFd+v++nsld+vsdRDf+iE+ +a al+m+hlsr++Eelil++s+ fgfv+l+d++++gss
  lcl|NCBI__GCF_002000365.1:WP_077278530.1 216 RYTAQLLGFDDVTDNSLDSVSDRDFAIEFCAAGALIMTHLSRFSEELILWASAQFGFVDLPDRFCTGSS 284
                                               ********************************************************************* PP

                                 TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345
                                               imPqKKnpDv El+Rgktgrv+Gnl++llt++K++PlaYnkD qEdke+lfd+++t+  +l++++ ++ 
  lcl|NCBI__GCF_002000365.1:WP_077278530.1 285 IMPQKKNPDVPELVRGKTGRVNGNLVALLTLMKGQPLAYNKDNQEDKEPLFDTVDTLAGSLRAFADMVP 353
                                               ********************************************************************* PP

                                 TIGR00838 346 elkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsek 414
                                               +++v+ e ++eaa+++fa+atdlAdylvr+G+PFR+ahe+vG++v++ +e+G +l e+ leelq +s+ 
  lcl|NCBI__GCF_002000365.1:WP_077278530.1 354 HIQVRAETMREAASRGFATATDLADYLVRRGMPFRDAHEVVGKAVRHGVETGRDLGEMRLEELQGFSKM 422
                                               ********************************************************************* PP

                                 TIGR00838 415 leedvlevldleeavekrdakGGtakeevekaieeakael 454
                                               +e dv++vl+le +v++r+++GGta+e+v  +i +a+ael
  lcl|NCBI__GCF_002000365.1:WP_077278530.1 423 IEADVFDVLTLEGSVAARNVHGGTAPEQVLARIRAARAEL 462
                                               ************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (467 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: 10.01
//
[ok]

This GapMind analysis is from Apr 10 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