Alignments for a candidate for argH in Nocardioides dokdonensis FR1436

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Nocardioides dokdonensis FR1436

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_068111469.1 I601_RS15180 argininosuccinate lyase

Query= BRENDA::P9WPY7
         (470 letters)



>NCBI__GCF_001653335.1:WP_068111469.1
          Length = 485

 Score =  611 bits (1576), Expect = e-179
 Identities = 318/474 (67%), Positives = 370/474 (78%), Gaps = 7/474 (1%)

Query: 2   STNEGSLWGGRFAGGPSDALAALSKSTHFDWVLAPYDLTASRAHTMVLFRAGLLTEEQRD 61
           +TN G LWGGRFAGGPS  L ALS+STHFDW L PYDL  SRAH   L R+GLLT     
Sbjct: 11  ATNTGKLWGGRFAGGPSPELEALSRSTHFDWRLTPYDLAGSRAHANALHRSGLLTAADHT 70

Query: 62  GLLAGLDSLAQDVADGSFGPLVTDEDVHAALERGLIDRVGPDLGGRLRAGRSRNDQVAAL 121
            LL GLD L +  A G   P  +DEDVH ALER L++ VG D+GGRLRAGRSRNDQ+A L
Sbjct: 71  ELLRGLDVLGERHAGGELHPDPSDEDVHGALERLLLEEVGVDIGGRLRAGRSRNDQIATL 130

Query: 122 FRMWLRDAVRRVATGVLDVVGALAEQAAAH------PSAIMPGKTHLQSAQPILLAHHLL 175
           F+++LRD  R VA  VLD+V ALA QA AH         IMPG+THLQ AQP+LLAHHLL
Sbjct: 131 FKVFLRDHARVVAAQVLDLVDALAGQARAHLGGEDAEPTIMPGRTHLQHAQPVLLAHHLL 190

Query: 176 AHAHPLLRDLDRIVDFDKR-AAVSPYGSGALAGSSLGLDPDAIAADLGFSAAADNSVDAT 234
           AHA PLLRD+DR+ D+D R AA SPYGSGALAG SLGLDP  +AA+LGFS ++ NS+D T
Sbjct: 191 AHAWPLLRDVDRLADWDARVAADSPYGSGALAGQSLGLDPTLVAAELGFSGSSANSIDGT 250

Query: 235 AARDFAAEAAFVFAMIAVDLSRLAEDIIVWSSTEFGYVTLHDSWSTGSSIMPQKKNPDIA 294
           +ARDF AE AFV A I +D+SRLAE++I+W++ EFG+VTLHDSWSTGSSIMPQKKNPDIA
Sbjct: 251 SARDFVAELAFVTAQIGIDVSRLAEEVILWATKEFGFVTLHDSWSTGSSIMPQKKNPDIA 310

Query: 295 ELARGKSGRLIGNLAGLLATLKAQPLAYNRDLQEDKEPVFDSVAQLELLLPAMAGLVASL 354
           ELARGK+GRLIGNLAGL+ATLKA PLAYNRDLQEDKEPVFDSV  LE+LLPA  G++A+L
Sbjct: 311 ELARGKAGRLIGNLAGLMATLKALPLAYNRDLQEDKEPVFDSVDTLEVLLPAFTGMIATL 370

Query: 355 TFNVQRMAELAPAGYTLATDLAEWLVRQGVPFRSAHEAAGAAVRAAEQRGVGLQELTDDE 414
            F+ +RMAELAP G++LATD+AEWLVRQ VPFR AHE AGA VR  E+  V L +L+D++
Sbjct: 371 EFDGERMAELAPQGFSLATDVAEWLVRQNVPFRVAHEVAGACVRRCEELDVELADLSDEQ 430

Query: 415 LAAISPELTPQVREVLTIEGSVSARDCRGGTAPGRVAEQLNAIGEAAERLRRQL 468
              ISPELTPQVREVLT  GSV++RD RGGTAP RV EQL+ +   A  LR  L
Sbjct: 431 FREISPELTPQVREVLTAGGSVASRDGRGGTAPVRVREQLDELVARAGGLREHL 484


Lambda     K      H
   0.318    0.133    0.382 

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: 689
Number of extensions: 31
Number of successful extensions: 3
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: 470
Length of database: 485
Length adjustment: 34
Effective length of query: 436
Effective length of database: 451
Effective search space:   196636
Effective search space used:   196636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_068111469.1 I601_RS15180 (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.677969.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-173  563.5   0.0   2.3e-173  563.3   0.0    1.0  1  NCBI__GCF_001653335.1:WP_068111469.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001653335.1:WP_068111469.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  563.3   0.0  2.3e-173  2.3e-173       1     452 [.      17     475 ..      17     478 .. 0.98

  Alignments for each domain:
  == domain 1  score: 563.3 bits;  conditional E-value: 2.3e-173
                             TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegkle 73 
                                           lwggR++++++++++++++s++fD++l+ +D+ gs ah++aL++ g+lt+ ++++l ++L+ l e  + g+l+
  NCBI__GCF_001653335.1:WP_068111469.1  17 LWGGRFAGGPSPELEALSRSTHFDWRLTPYDLAGSRAHANALHRSGLLTAADHTELLRGLDVLGERHAGGELH 89 
                                           7************************************************************************ PP

                             TIGR00838  74 levdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAeke.. 144
                                           +++++eD+H a+Er l ++vg d+g++l++grsRnDq+at ++++lrd+ + +a +++dl++al+ +A+++  
  NCBI__GCF_001653335.1:WP_068111469.1  90 PDPSDEDVHGALERLLLEEVGVDIGGRLRAGRSRNDQIATLFKVFLRDHARVVAAQVLDLVDALAGQARAHlg 162
                                           *******************************************************************987633 PP

                             TIGR00838 145 ....vetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvn.ksPlGsgAlagtsfeidrellae 212
                                               + t+mpg tHLq+AqP+ laHhlla+a+ l rD++Rl d   Rv+  sP+GsgAlag+s+++d++l+a+
  NCBI__GCF_001653335.1:WP_068111469.1 163 gedaEPTIMPGRTHLQHAQPVLLAHHLLAHAWPLLRDVDRLADWDARVAaDSPYGSGALAGQSLGLDPTLVAA 235
                                           3222579****************************************96369********************* PP

                             TIGR00838 213 lLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpD 285
                                            LgF+   +ns+d++s+RDf++El +++a + +++srlaEe+il++++Efgfv+l+d++s+gssimPqKKnpD
  NCBI__GCF_001653335.1:WP_068111469.1 236 ELGFSGSSANSIDGTSARDFVAELAFVTAQIGIDVSRLAEEVILWATKEFGFVTLHDSWSTGSSIMPQKKNPD 308
                                           ************************************************************************* PP

                             TIGR00838 286 vaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaa 358
                                           +aEl+Rgk+gr+iGnl+gl+++lKalPlaYn+DlqEdke++fd+++t+e ll ++tg++++l++  er++e+a
  NCBI__GCF_001653335.1:WP_068111469.1 309 IAELARGKAGRLIGNLAGLMATLKALPLAYNRDLQEDKEPVFDSVDTLEVLLPAFTGMIATLEFDGERMAELA 381
                                           ************************************************************************* PP

                             TIGR00838 359 kknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavek 431
                                            ++f+latd+A++lvr+ vPFR ahe++G++v++++e  ++l +l+ e+++++s++l+++v+evl+   +v+ 
  NCBI__GCF_001653335.1:WP_068111469.1 382 PQGFSLATDVAEWLVRQNVPFRVAHEVAGACVRRCEELDVELADLSDEQFREISPELTPQVREVLTAGGSVAS 454
                                           ************************************************************************* PP

                             TIGR00838 432 rdakGGtakeevekaieeaka 452
                                           rd +GGta+ +v+++++e+ a
  NCBI__GCF_001653335.1:WP_068111469.1 455 RDGRGGTAPVRVREQLDELVA 475
                                           ***************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (485 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 30.22
//
[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