Alignments for a candidate for argH in Thioalkalivibrio halophilus HL17

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Thioalkalivibrio halophilus HL17

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate WP_077244050.1 B1A74_RS05800 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>NCBI__GCF_001995255.1:WP_077244050.1
          Length = 477

 Score =  459 bits (1181), Expect = e-134
 Identities = 238/458 (51%), Positives = 308/458 (67%), Gaps = 1/458 (0%)

Query: 2   TKEQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQL 61
           ++ + W  RF       + RF AS+ FD  L   D+ GSQAHA MLA  G++S +E  ++
Sbjct: 12  SEAKLWGGRFSEPTDAFVERFTASVDFDRRLYREDIRGSQAHAHMLARVGVLSEDEARRI 71

Query: 62  VAGLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRL 121
           V GL+ IR E   G+F   V  EDVH  +E RL E +GDVGKKLHT RSRNDQ+ TD RL
Sbjct: 72  VDGLDVIRDEIAAGEFDWQVGREDVHMNIEARLIERIGDVGKKLHTGRSRNDQIATDIRL 131

Query: 122 YLRDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRD 181
           +LR  I +I   +R +Q  L+D+AE+  +T++PG+THLQ AQPV+  HH+LA+++M +RD
Sbjct: 132 WLRAAIDEIIELIRSYQSGLVDLAEREADTIMPGFTHLQTAQPVTFGHHMLAWYEMLERD 191

Query: 182 WERLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFL 241
            ERL D  RRVN+ PLG  ALAGT +P+DR Y A+ L FD +  NSLD VSDRDFAIEF 
Sbjct: 192 AERLRDCRRRVNVLPLGAAALAGTPYPLDREYVAEQLGFDGVTRNSLDAVSDRDFAIEFT 251

Query: 242 CAASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRV 301
            AAS +M+HLSR AEE++LW+S +F F+ L D   TGSSIMPQKKNPDVPELVRGKTGRV
Sbjct: 252 AAASTLMMHLSRQAEELVLWTSAQFDFIELPDRYCTGSSIMPQKKNPDVPELVRGKTGRV 311

Query: 302 FGHLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQ 361
           +GHL ++L +MK  PLAYNKD QEDKE LFD+V+T+  SL A   ++   L  R      
Sbjct: 312 YGHLTSLLTLMKSQPLAYNKDNQEDKEPLFDTVDTLLGSLRAFADMV-PNLAVRRANTLA 370

Query: 362 AVTEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFA 421
           A T  F+ ATD+ADYL  RGV FR+A+ +VG+ V+ +   G  L  L L E QQL  A  
Sbjct: 371 ATTRGFATATDLADYLVERGVAFRDAHEVVGRAVRLAQERGVDLAQLSLGELQQLSAAVG 430

Query: 422 ADIYEAISPRQVVAARNSHGGTGFVQVSKALIAARAQI 459
            D++  ++    VAAR   GGT   QV + + AARA++
Sbjct: 431 EDVHGVLTAEGSVAARRVTGGTAPEQVRRQVAAARARL 468


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: 569
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: 461
Length of database: 477
Length adjustment: 33
Effective length of query: 428
Effective length of database: 444
Effective search space:   190032
Effective search space used:   190032
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_077244050.1 B1A74_RS05800 (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.26853.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-197  641.8   0.0   3.9e-197  641.7   0.0    1.0  1  lcl|NCBI__GCF_001995255.1:WP_077244050.1  B1A74_RS05800 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001995255.1:WP_077244050.1  B1A74_RS05800 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  641.7   0.0  3.9e-197  3.9e-197       1     454 [.      16     468 ..      16     469 .. 1.00

  Alignments for each domain:
  == domain 1  score: 641.7 bits;  conditional E-value: 3.9e-197
                                 TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 
                                               lwggR+++ +d  v++f+as++fD +l+++Di+gs ah+++La++g+l+e+ea++++++L+ +++e+++
  lcl|NCBI__GCF_001995255.1:WP_077244050.1  16 LWGGRFSEPTDAFVERFTASVDFDRRLYREDIRGSQAHAHMLARVGVLSEDEARRIVDGLDVIRDEIAA 84 
                                               7******************************************************************** PP

                                 TIGR00838  70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138
                                               g+++++v  eD+H+++E++li+++g dvgkklhtgrsRnDq+atd+rl+lr++++e++e ++  ++ lv
  lcl|NCBI__GCF_001995255.1:WP_077244050.1  85 GEFDWQVGREDVHMNIEARLIERIG-DVGKKLHTGRSRNDQIATDIRLWLRAAIDEIIELIRSYQSGLV 152
                                               *************************.******************************************* PP

                                 TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207
                                               ++Ae+e +t+mpg+tHLq AqP+t++Hh+la+ emlerD eRl d  +Rvn+ PlG++Alagt +++dr
  lcl|NCBI__GCF_001995255.1:WP_077244050.1 153 DLAEREADTIMPGFTHLQTAQPVTFGHHMLAWYEMLERDAERLRDCRRRVNVLPLGAAALAGTPYPLDR 221
                                               ********************************************************************* PP

                                 TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276
                                               e++ae+LgFd v++nsldavsdRDf+iE+ +aa+ lm+hlsr aEel+l++s+ f+f+el+d++++gss
  lcl|NCBI__GCF_001995255.1:WP_077244050.1 222 EYVAEQLGFDGVTRNSLDAVSDRDFAIEFTAAASTLMMHLSRQAEELVLWTSAQFDFIELPDRYCTGSS 290
                                               ********************************************************************* PP

                                 TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345
                                               imPqKKnpDv El+Rgktgrv+G+lt+llt++K++PlaYnkD qEdke+lfd+++t+  +l++++ ++ 
  lcl|NCBI__GCF_001995255.1:WP_077244050.1 291 IMPQKKNPDVPELVRGKTGRVYGHLTSLLTLMKSQPLAYNKDNQEDKEPLFDTVDTLLGSLRAFADMVP 359
                                               ********************************************************************* PP

                                 TIGR00838 346 elkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsek 414
                                               +l v++ ++  a++++fa+atdlAdylv++Gv FR+ahe+vG++v+ a e+G++l +l+l elq+ls +
  lcl|NCBI__GCF_001995255.1:WP_077244050.1 360 NLAVRRANTLAATTRGFATATDLADYLVERGVAFRDAHEVVGRAVRLAQERGVDLAQLSLGELQQLSAA 428
                                               ********************************************************************* PP

                                 TIGR00838 415 leedvlevldleeavekrdakGGtakeevekaieeakael 454
                                               + edv+ vl+ e +v++r+++GGta+e+v++++++a+a+l
  lcl|NCBI__GCF_001995255.1:WP_077244050.1 429 VGEDVHGVLTAEGSVAARRVTGGTAPEQVRRQVAAARARL 468
                                               *************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (477 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: 00:00:00.03
# Mc/sec: 7.18
//
[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