Alignments for a candidate for argH in Desulfacinum hydrothermale DSM 13146

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Desulfacinum hydrothermale DSM 13146

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_084056570.1 B9A12_RS04105 argininosuccinate lyase

Query= BRENDA::Q8DVX5
         (460 letters)



>NCBI__GCF_900176285.1:WP_084056570.1
          Length = 472

 Score =  456 bits (1174), Expect = e-133
 Identities = 228/455 (50%), Positives = 313/455 (68%), Gaps = 1/455 (0%)

Query: 5   NHKLWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAATIK 64
           + KLW GRF+    + VEE+ ASI FD +L  +D++GSIAH  ML + GIIS ++A+ I 
Sbjct: 2   SEKLWQGRFDQPTDKMVEEYTASIHFDSRLYRYDIEGSIAHCRMLADCGIISHDEASQIV 61

Query: 65  AGLEDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMHLY 124
             L ++  E + G+L  D S EDIHM +E  L  KIG V GKLHTARSRNDQ+A D  LY
Sbjct: 62  QALGEIRRETERGELNLDPSQEDIHMAVEQRLMQKIGEVGGKLHTARSRNDQIALDTRLY 121

Query: 125 LKAKLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTRDS 184
           ++  L +    L ++ T L DLA+K++H I+PG+THLQHAQP+   HHL+AY  MF RD 
Sbjct: 122 MRDVLLQCRRLLLDVITGLTDLAEKNLHVILPGFTHLQHAQPVLLAHHLLAYCEMFLRDE 181

Query: 185 ERFIFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEFLS 244
           ER       T++ PLG+AALAGTTFPID E TA+ +GF     NS+DAVSDRD+++EF +
Sbjct: 182 ERMAQCFNRTNVMPLGSAALAGTTFPIDMERTARQLGFPRVIRNSMDAVSDRDYLIEFCA 241

Query: 245 NASILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGRVY 304
             ++ MMH+SR+ EE++ W S E+ FV +SD F TGSSIMPQKKNPD+ EL+RGK+GR+Y
Sbjct: 242 AGALAMMHISRLSEELVLWSSPEFDFVEISDAFCTGSSIMPQKKNPDVPELMRGKTGRIY 301

Query: 305 ANLFGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAEST 364
            NL  LLT+ K LPL YN+DLQEDKE  FDTA+T+   L +L  ML ++  +++ M ++ 
Sbjct: 302 GNLMALLTLTKGLPLTYNRDLQEDKEPAFDTADTLLSTLAVLNKMLPALQFHEEKMVQAA 361

Query: 365 QKDFSNATELADYLASKGMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLIEED 424
            + F+ AT++ADYL  KG+PFR+AH +VG+L+  C + G  L D  L+  +     +EED
Sbjct: 362 AQSFALATDVADYLVLKGVPFRKAHHVVGQLVSHCIREGKDLSDCTLDELKKFHKALEED 421

Query: 425 VYETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKA 459
           ++  L   +AV+RR SLGGT  E+V+ +  EA +A
Sbjct: 422 IFSILDIRSAVDRRRSLGGTSTERVR-EALEATRA 455


Lambda     K      H
   0.318    0.132    0.378 

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: 559
Number of extensions: 14
Number of successful extensions: 1
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: 460
Length of database: 472
Length adjustment: 33
Effective length of query: 427
Effective length of database: 439
Effective search space:   187453
Effective search space used:   187453
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_084056570.1 B9A12_RS04105 (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.8151.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.2e-198  643.9   0.1   9.4e-198  643.7   0.1    1.0  1  lcl|NCBI__GCF_900176285.1:WP_084056570.1  B9A12_RS04105 argininosuccinate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176285.1:WP_084056570.1  B9A12_RS04105 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  643.7   0.1  9.4e-198  9.4e-198       1     454 [.       5     457 ..       5     458 .. 1.00

  Alignments for each domain:
  == domain 1  score: 643.7 bits;  conditional E-value: 9.4e-198
                                 TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 
                                               lw+gR+++ +dk v+e++as++fD +l+++Diegsiah ++La +gi++++ea+++++aL e+++e+++
  lcl|NCBI__GCF_900176285.1:WP_084056570.1   5 LWQGRFDQPTDKMVEEYTASIHFDSRLYRYDIEGSIAHCRMLADCGIISHDEASQIVQALGEIRRETER 73 
                                               7******************************************************************** PP

                                 TIGR00838  70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138
                                               g+l+l++++eDiH+avE++l++k+g +vg+klht+rsRnDq+a d rly+rd + + ++ l+d+++ l 
  lcl|NCBI__GCF_900176285.1:WP_084056570.1  74 GELNLDPSQEDIHMAVEQRLMQKIG-EVGGKLHTARSRNDQIALDTRLYMRDVLLQCRRLLLDVITGLT 141
                                               *************************.******************************************* PP

                                 TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207
                                               ++Aek+ ++++pg+tHLq+AqP+ laHhllay em+ rD eR+ + ++R+n+ PlGs+Alagt+f+id 
  lcl|NCBI__GCF_900176285.1:WP_084056570.1 142 DLAEKNLHVILPGFTHLQHAQPVLLAHHLLAYCEMFLRDEERMAQCFNRTNVMPLGSAALAGTTFPIDM 210
                                               ********************************************************************* PP

                                 TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276
                                               e++a++LgF +v++ns+davsdRD++iE+ +a al+m+h+srl+Eel+l+ss Ef+fve+sd++++gss
  lcl|NCBI__GCF_900176285.1:WP_084056570.1 211 ERTARQLGFPRVIRNSMDAVSDRDYLIEFCAAGALAMMHISRLSEELVLWSSPEFDFVEISDAFCTGSS 279
                                               ********************************************************************* PP

                                 TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345
                                               imPqKKnpDv El+Rgktgr++Gnl++llt+ K+lPl+Yn+DlqEdke+ fd+ +t+ ++l v++ +l 
  lcl|NCBI__GCF_900176285.1:WP_084056570.1 280 IMPQKKNPDVPELMRGKTGRIYGNLMALLTLTKGLPLTYNRDLQEDKEPAFDTADTLLSTLAVLNKMLP 348
                                               ********************************************************************* PP

                                 TIGR00838 346 elkvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsek 414
                                                l++++e++ +aa+++falatd+Adylv kGvPFR+ah++vG++v ++i++Gk+l++ tl+el+k++++
  lcl|NCBI__GCF_900176285.1:WP_084056570.1 349 ALQFHEEKMVQAAAQSFALATDVADYLVLKGVPFRKAHHVVGQLVSHCIREGKDLSDCTLDELKKFHKA 417
                                               ********************************************************************* PP

                                 TIGR00838 415 leedvlevldleeavekrdakGGtakeevekaieeakael 454
                                               leed++++ld+++av++r++ GGt+ e+v++a+e+++a++
  lcl|NCBI__GCF_900176285.1:WP_084056570.1 418 LEEDIFSILDIRSAVDRRRSLGGTSTERVREALEATRADV 457
                                               **********************************999876 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.77
//
[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