Alignments for a candidate for argH in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Thermomonospora curvata DSM 43183

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_012852508.1 TCUR_RS10675 argininosuccinate lyase

Query= BRENDA::P9WPY7
         (470 letters)



>NCBI__GCF_000024385.1:WP_012852508.1
          Length = 472

 Score =  527 bits (1358), Expect = e-154
 Identities = 270/454 (59%), Positives = 334/454 (73%), Gaps = 1/454 (0%)

Query: 1   MSTNEGSLWGGRFAGGPSDALAALSKSTHFDWVLAPYDLTASRAHTMVLFRAGLLTEEQR 60
           MS     LWGGRF GGPS+ALA LS S  FDW LAPYDL  SRAH  VL RAGLLT+E+ 
Sbjct: 1   MSKAPTRLWGGRFEGGPSEALARLSVSVQFDWRLAPYDLMGSRAHARVLHRAGLLTDEEL 60

Query: 61  DGLLAGLDSLAQDVADGSFGPLVTDEDVHAALERGLIDRVGPDLGGRLRAGRSRNDQVAA 120
             +L  LD L Q    G F P V DEDVH ALERGL++R+G  LGG+LRAGRSRNDQVA 
Sbjct: 61  TRMLGALDDLEQACRSGEFRPTVADEDVHTALERGLLERLG-SLGGKLRAGRSRNDQVAT 119

Query: 121 LFRMWLRDAVRRVATGVLDVVGALAEQAAAHPSAIMPGKTHLQSAQPILLAHHLLAHAHP 180
             R++LRD VR++ + ++++  AL  QA  +     PG THLQ AQP+L +H LLAH HP
Sbjct: 120 DLRLYLRDHVRQIVSRLVELETALIAQAEHNLDVAAPGMTHLQHAQPVLFSHQLLAHVHP 179

Query: 181 LLRDLDRIVDFDKRAAVSPYGSGALAGSSLGLDPDAIAADLGFSAAADNSVDATAARDFA 240
           L RD+DR+ D+DKRAA+ P G+GALAGSSL LDP A+A +LGF A A NS+DA + RDFA
Sbjct: 180 LARDIDRLRDWDKRAAICPLGAGALAGSSLPLDPKAVAEELGFDAPAANSMDAVSDRDFA 239

Query: 241 AEAAFVFAMIAVDLSRLAEDIIVWSSTEFGYVTLHDSWSTGSSIMPQKKNPDIAELARGK 300
           AE  F  AMI V LSRL E+I++W+S EF ++ + D+++TGSSIMPQKKNPD+AELARGK
Sbjct: 240 AEFLFAAAMIGVHLSRLGEEIVLWASQEFRWIEMDDAYATGSSIMPQKKNPDVAELARGK 299

Query: 301 SGRLIGNLAGLLATLKAQPLAYNRDLQEDKEPVFDSVAQLELLLPAMAGLVASLTFNVQR 360
           +GRLIG+L GLL TLK  PL YNRDLQEDKE VFD+V  L L+LPAM+GL+A++  N +R
Sbjct: 300 AGRLIGHLVGLLTTLKGLPLTYNRDLQEDKEGVFDAVETLLLVLPAMSGLIATMRVNTER 359

Query: 361 MAELAPAGYTLATDLAEWLVRQGVPFRSAHEAAGAAVRAAEQRGVGLQELTDDELAAISP 420
           + + AP G+ LATDLAE LVR+GVPFR AHE  G  V   +       +LTD+ELA +SP
Sbjct: 360 LEDTAPEGFALATDLAELLVRRGVPFREAHEVVGHLVVWCQVHDKDFGDLTDEELAKVSP 419

Query: 421 ELTPQVREVLTIEGSVSARDCRGGTAPGRVAEQL 454
            LTP VREVL ++G++++R   GGT+P RV EQL
Sbjct: 420 HLTPDVREVLNVQGALASRKAHGGTSPERVREQL 453


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: 615
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: 472
Length adjustment: 33
Effective length of query: 437
Effective length of database: 439
Effective search space:   191843
Effective search space used:   191843
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_012852508.1 TCUR_RS10675 (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.15230.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-184  599.0   0.0   3.8e-184  598.8   0.0    1.0  1  lcl|NCBI__GCF_000024385.1:WP_012852508.1  TCUR_RS10675 argininosuccinate l


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024385.1:WP_012852508.1  TCUR_RS10675 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  598.8   0.0  3.8e-184  3.8e-184       1     453 [.       8     459 ..       8     461 .. 0.99

  Alignments for each domain:
  == domain 1  score: 598.8 bits;  conditional E-value: 3.8e-184
                                 TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 
                                               lwggR+++++++a+a+++ s++fD++la +D+ gs ah+++L++ag+lt+ee +++  aL++l++ +++
  lcl|NCBI__GCF_000024385.1:WP_012852508.1   8 LWGGRFEGGPSEALARLSVSVQFDWRLAPYDLMGSRAHARVLHRAGLLTDEELTRMLGALDDLEQACRS 76 
                                               7******************************************************************** PP

                                 TIGR00838  70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138
                                               g+++++v +eD+H+a+Er l +++g  +g+kl++grsRnDqvatdlrlylrd+v++++++l +l +al+
  lcl|NCBI__GCF_000024385.1:WP_012852508.1  77 GEFRPTVADEDVHTALERGLLERLG-SLGGKLRAGRSRNDQVATDLRLYLRDHVRQIVSRLVELETALI 144
                                               *************************.******************************************* PP

                                 TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207
                                                +Ae++ ++  pg tHLq+AqP+ ++H lla+++ l+rD++Rl d  kR++ +PlG+gAlag+s+++d+
  lcl|NCBI__GCF_000024385.1:WP_012852508.1 145 AQAEHNLDVAAPGMTHLQHAQPVLFSHQLLAHVHPLARDIDRLRDWDKRAAICPLGAGALAGSSLPLDP 213
                                               ********************************************************************* PP

                                 TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276
                                               +++ae LgFda ++ns+davsdRDf++E+l+aaa++ vhlsrl Ee++l++s+Ef ++e++d++++gss
  lcl|NCBI__GCF_000024385.1:WP_012852508.1 214 KAVAEELGFDAPAANSMDAVSDRDFAAEFLFAAAMIGVHLSRLGEEIVLWASQEFRWIEMDDAYATGSS 282
                                               ********************************************************************* PP

                                 TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345
                                               imPqKKnpDvaEl+Rgk+gr+iG+l+gllt+lK+lPl+Yn+DlqEdke++fda++t+  +l ++ gl++
  lcl|NCBI__GCF_000024385.1:WP_012852508.1 283 IMPQKKNPDVAELARGKAGRLIGHLVGLLTTLKGLPLTYNRDLQEDKEGVFDAVETLLLVLPAMSGLIA 351
                                               ********************************************************************* PP

                                 TIGR00838 346 elkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsek 414
                                               +++vn+erle+ a ++falatdlA++lvr+GvPFReahe+vG++v+ +  + k++ +lt eel+k+s++
  lcl|NCBI__GCF_000024385.1:WP_012852508.1 352 TMRVNTERLEDTAPEGFALATDLAELLVRRGVPFREAHEVVGHLVVWCQVHDKDFGDLTDEELAKVSPH 420
                                               *************************************************999***************** PP

                                 TIGR00838 415 leedvlevldleeavekrdakGGtakeevekaieeakae 453
                                               l++dv+evl+++ a++ r+a+GGt++e+v+++++e++a 
  lcl|NCBI__GCF_000024385.1:WP_012852508.1 421 LTPDVREVLNVQGALASRKAHGGTSPERVREQLAELRAL 459
                                               **********************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (472 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: 00:00:00.02
# Mc/sec: 8.54
//
[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