GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argH in Streptacidiphilus oryzae TH49

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_084703910.1 BS73_RS08890 argininosuccinate lyase

Query= BRENDA::P9WPY7
         (470 letters)



>NCBI__GCF_000744815.1:WP_084703910.1
          Length = 494

 Score =  607 bits (1564), Expect = e-178
 Identities = 307/462 (66%), Positives = 368/462 (79%), Gaps = 1/462 (0%)

Query: 8   LWGGRFAGGPSDALAALSKSTHFDWVLAPYDLTASRAHTMVLFRAGLLTEEQRDGLLAGL 67
           LWGGRFA GPS+ALAALS S HFDW LAPYD+  SRAH  VL +AGLLT+E+ + +LAGL
Sbjct: 31  LWGGRFADGPSEALAALSASVHFDWRLAPYDIAGSRAHARVLHKAGLLTDEELERMLAGL 90

Query: 68  DSLAQDVADGSFGPLVTDEDVHAALERGLIDRVGPDLGGRLRAGRSRNDQVAALFRMWLR 127
           D L  DV  G F   V DEDVH ALERGL++R+GP+LGG+LRAGRSRNDQ+A L RM+LR
Sbjct: 91  DRLLADVESGDFVGTVADEDVHTALERGLLERLGPELGGKLRAGRSRNDQIATLGRMYLR 150

Query: 128 DAVRRVATGVLDVVGALAEQAAAHPSAIMPGKTHLQSAQPILLAHHLLAHAHPLLRDLDR 187
           D  R V   +L++  AL   A AHP A MPG+THLQ AQP+L AHH+LAH   L RD +R
Sbjct: 151 DHGRTVGRLLLELQEALVGLAEAHPKAAMPGRTHLQHAQPVLFAHHMLAHVAALGRDAER 210

Query: 188 IVDFDKRAAVSPYGSGALAGSSLGLDPDAIAADLGFS-AAADNSVDATAARDFAAEAAFV 246
           +  +D+R AVSPYGSGALAGSSLGLDP+A+AA+LGF   ++ NS+D TAARD+ AE AFV
Sbjct: 211 LRQWDERTAVSPYGSGALAGSSLGLDPEAVAAELGFERGSSGNSIDGTAARDYVAEFAFV 270

Query: 247 FAMIAVDLSRLAEDIIVWSSTEFGYVTLHDSWSTGSSIMPQKKNPDIAELARGKSGRLIG 306
            AMI +DLSR+AE+II+W++ EFG++TLHD++STGSSIMPQKKNPDIAELARGKSGRLIG
Sbjct: 271 TAMIGIDLSRIAEEIILWNTKEFGFITLHDAFSTGSSIMPQKKNPDIAELARGKSGRLIG 330

Query: 307 NLAGLLATLKAQPLAYNRDLQEDKEPVFDSVAQLELLLPAMAGLVASLTFNVQRMAELAP 366
           NL GLLATLKA PLAYNRDLQEDKEPVFDSV  LE+LLPA  G++A+LT + +RMAELAP
Sbjct: 331 NLTGLLATLKALPLAYNRDLQEDKEPVFDSVDTLEVLLPAFIGMMATLTVHEERMAELAP 390

Query: 367 AGYTLATDLAEWLVRQGVPFRSAHEAAGAAVRAAEQRGVGLQELTDDELAAISPELTPQV 426
           AG++LATD+AEWLVRQG PFR AHE AGA V+  E RG+ L +LTD + A ISP LTP+V
Sbjct: 391 AGFSLATDIAEWLVRQGTPFRVAHEVAGACVKFCEPRGLELSDLTDAQFAEISPLLTPEV 450

Query: 427 REVLTIEGSVSARDCRGGTAPGRVAEQLNAIGEAAERLRRQL 468
           R VLT+EG++++RD RGGTAP  VA QL  +     R R  L
Sbjct: 451 RSVLTVEGAIASRDGRGGTAPAAVARQLTEVAADLARQREWL 492


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: 677
Number of extensions: 30
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: 470
Length of database: 494
Length adjustment: 34
Effective length of query: 436
Effective length of database: 460
Effective search space:   200560
Effective search space used:   200560
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: 52 (24.6 bits)

Align candidate WP_084703910.1 BS73_RS08890 (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.737764.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.7e-182  590.9   0.0   1.1e-181  590.7   0.0    1.0  1  NCBI__GCF_000744815.1:WP_084703910.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_084703910.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  590.7   0.0  1.1e-181  1.1e-181       1     454 [.      31     485 ..      31     486 .. 0.99

  Alignments for each domain:
  == domain 1  score: 590.7 bits;  conditional E-value: 1.1e-181
                             TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegkle 73 
                                           lwggR+++++++a+a+++as++fD++la +Di gs ah+++L+kag+lt+ee +++ ++L++l  +v++g++ 
  NCBI__GCF_000744815.1:WP_084703910.1  31 LWGGRFADGPSEALAALSASVHFDWRLAPYDIAGSRAHARVLHKAGLLTDEELERMLAGLDRLLADVESGDFV 103
                                           7************************************************************************ PP

                             TIGR00838  74 levdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekeve 146
                                            +v +eD+H+a+Er l +++g ++g+kl++grsRnDq+at  r+ylrd+ +++ + l++l++alv +Ae++ +
  NCBI__GCF_000744815.1:WP_084703910.1 104 GTVADEDVHTALERGLLERLGPELGGKLRAGRSRNDQIATLGRMYLRDHGRTVGRLLLELQEALVGLAEAHPK 176
                                           ************************************************************************* PP

                             TIGR00838 147 tlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFda. 218
                                           + mpg tHLq+AqP+ +aHh+la++ +l rD eRl +  +R+++sP+GsgAlag+s+++d+e++a+ LgF++ 
  NCBI__GCF_000744815.1:WP_084703910.1 177 AAMPGRTHLQHAQPVLFAHHMLAHVAALGRDAERLRQWDERTAVSPYGSGALAGSSLGLDPEAVAAELGFERg 249
                                           **********************************************************************973 PP

                             TIGR00838 219 vvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliR 291
                                              ns+d++++RD+++E+ +++a++ ++lsr+aEe+il++++Efgf++l+d++s+gssimPqKKnpD+aEl+R
  NCBI__GCF_000744815.1:WP_084703910.1 250 SSGNSIDGTAARDYVAEFAFVTAMIGIDLSRIAEEIILWNTKEFGFITLHDAFSTGSSIMPQKKNPDIAELAR 322
                                           678********************************************************************** PP

                             TIGR00838 292 gktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfal 364
                                           gk+gr+iGnltgll++lKalPlaYn+DlqEdke++fd+++t+e ll ++ g++++l+v++er++e+a ++f+l
  NCBI__GCF_000744815.1:WP_084703910.1 323 GKSGRLIGNLTGLLATLKALPLAYNRDLQEDKEPVFDSVDTLEVLLPAFIGMMATLTVHEERMAELAPAGFSL 395
                                           ************************************************************************* PP

                             TIGR00838 365 atdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGG 437
                                           atd+A++lvr+G PFR ahe++G++v+ ++ +G++l++lt ++++++s+ l+++v++vl++e a++ rd +GG
  NCBI__GCF_000744815.1:WP_084703910.1 396 ATDIAEWLVRQGTPFRVAHEVAGACVKFCEPRGLELSDLTDAQFAEISPLLTPEVRSVLTVEGAIASRDGRGG 468
                                           ************************************************************************* PP

                             TIGR00838 438 takeevekaieeakael 454
                                           ta+++v++++ e+ a+l
  NCBI__GCF_000744815.1:WP_084703910.1 469 TAPAAVARQLTEVAADL 485
                                           **********9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (494 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 17.49
//
[ok]

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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