Alignments for a candidate for argH in Methylocella silvestris BL2

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Methylocella silvestris BL2

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate WP_012590227.1 MSIL_RS06120 argininosuccinate lyase

Query= ecocyc::ARGSUCCINLYA-MONOMER
         (457 letters)



>NCBI__GCF_000021745.1:WP_012590227.1
          Length = 466

 Score =  421 bits (1081), Expect = e-122
 Identities = 226/446 (50%), Positives = 295/446 (66%), Gaps = 2/446 (0%)

Query: 3   LWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEEAL 62
           +WGGRF    D   ++ N S+ FDYRLA QDI GS A    L  VG+++A++ A + + L
Sbjct: 5   MWGGRFASGPDAIMEEINASIGFDYRLAMQDIAGSKAHVAMLADVGIVSADDAADITQGL 64

Query: 63  NVLLEDVRARPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLWCK 122
             +  ++ +       +  EDIH  VE +L   +G    +LHT RSRNDQVA D +LW +
Sbjct: 65  EAIKAEIESGAFTFSRA-LEDIHMNVESRLAALIGPAAGRLHTARSRNDQVALDFRLWVR 123

Query: 123 DTVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDESR 182
           DT+  L    R LQ AL E A+    AVMPG+TH+Q AQPVTF H  LAYVEM ARD SR
Sbjct: 124 DTIDALDGQLRGLQLALAEKAKLYAGAVMPGFTHMQSAQPVTFGHHLLAYVEMFARDRSR 183

Query: 183 LQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLSAA 242
           L+DA  RL+ SPLG  ALAGT++ IDR   A  LGF   T NSLDSVSDRD VLE LSAA
Sbjct: 184 LRDARARLNESPLGAAALAGTSFPIDRHATARALGFDRPTANSLDSVSDRDFVLETLSAA 243

Query: 243 AIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQGA 302
           AI  VHLSRFAE+++ ++T + GF  LSD+ ++GSS+MPQK+NPDA EL+RGK GRV GA
Sbjct: 244 AIAAVHLSRFAEEIVLWSTPQFGFARLSDKFSTGSSIMPQKRNPDAAELVRGKAGRVIGA 303

Query: 303 LTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCQEAAQQ 362
           LTG+++ +KGLPL Y+KDMQEDKEG FDAL +   CL     ++  I+    R + AA  
Sbjct: 304 LTGLLVVMKGLPLTYSKDMQEDKEGAFDALHSLSLCLAAMTGMVKDIEPDTERMKAAAGA 363

Query: 363 GYANATELADYLV-AKGVPFREAHHIVGEAVVEAIRQGKPLEDLPLSELQKFSQVIDEDV 421
           GYA AT+LAD+LV A G+PFREAHH+ G  V  A  Q K LE+L L+E+Q     I+  V
Sbjct: 364 GYATATDLADWLVKALGLPFREAHHVTGRLVAAASAQDKGLEELALAEMQAVEPRINAGV 423

Query: 422 YPILSLQSCLDKRAAKGGVSPQQVAQ 447
           + +L +++ +  R + GG +P  V++
Sbjct: 424 FAVLGVENSVRSRMSYGGTAPANVSE 449


Lambda     K      H
   0.318    0.133    0.386 

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: 516
Number of extensions: 19
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: 457
Length of database: 466
Length adjustment: 33
Effective length of query: 424
Effective length of database: 433
Effective search space:   183592
Effective search space used:   183592
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_012590227.1 MSIL_RS06120 (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.6600.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.1e-185  601.4   0.0   7.4e-185  601.2   0.0    1.0  1  lcl|NCBI__GCF_000021745.1:WP_012590227.1  MSIL_RS06120 argininosuccinate l


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021745.1:WP_012590227.1  MSIL_RS06120 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  601.2   0.0  7.4e-185  7.4e-185       1     448 [.       5     452 ..       5     458 .. 0.99

  Alignments for each domain:
  == domain 1  score: 601.2 bits;  conditional E-value: 7.4e-185
                                 TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevke 69 
                                               +wggR+++++d  ++e nas+ fD++la +Di gs+ah+++La +gi+++++a++++++Le +k e+++
  lcl|NCBI__GCF_000021745.1:WP_012590227.1   5 MWGGRFASGPDAIMEEINASIGFDYRLAMQDIAGSKAHVAMLADVGIVSADDAADITQGLEAIKAEIES 73 
                                               6******************************************************************** PP

                                 TIGR00838  70 gklelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalv 138
                                               g+++++   eDiH++vE++l + +g  ++++lht+rsRnDqva d+rl++rd+++ l  +l+ l+ al+
  lcl|NCBI__GCF_000021745.1:WP_012590227.1  74 GAFTFSRALEDIHMNVESRLAALIG-PAAGRLHTARSRNDQVALDFRLWVRDTIDALDGQLRGLQLALA 141
                                               *************************.7778*************************************** PP

                                 TIGR00838 139 ekAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidr 207
                                               ekA+    ++mpg+tH+q+AqP+t++Hhllay+em++rD +Rl da  R+n+sPlG++Alagtsf+idr
  lcl|NCBI__GCF_000021745.1:WP_012590227.1 142 EKAKLYAGAVMPGFTHMQSAQPVTFGHHLLAYVEMFARDRSRLRDARARLNESPLGAAALAGTSFPIDR 210
                                               ********************************************************************* PP

                                 TIGR00838 208 ellaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgss 276
                                               +++a+ LgFd+ ++nsld+vsdRDf++E+lsaaa+++vhlsr+aEe++l+s+  fgf  lsd++s+gss
  lcl|NCBI__GCF_000021745.1:WP_012590227.1 211 HATARALGFDRPTANSLDSVSDRDFVLETLSAAAIAAVHLSRFAEEIVLWSTPQFGFARLSDKFSTGSS 279
                                               ********************************************************************* PP

                                 TIGR00838 277 imPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllk 345
                                               imPqK+npD+aEl+Rgk+grviG ltgll+++K+lPl+Y kD+qEdke+ fdal+ ++ +l ++tg++k
  lcl|NCBI__GCF_000021745.1:WP_012590227.1 280 IMPQKRNPDAAELVRGKAGRVIGALTGLLVVMKGLPLTYSKDMQEDKEGAFDALHSLSLCLAAMTGMVK 348
                                               ********************************************************************* PP

                                 TIGR00838 346 elkvnkerleeaakknfalatdlAdylvrk.GvPFReaheivGevvakaiekGkkleeltleelqklse 413
                                               +++  +er++ aa +++a+atdlAd+lv+  G+PFReah+++G++va+a ++ k+leel+l+e+q++++
  lcl|NCBI__GCF_000021745.1:WP_012590227.1 349 DIEPDTERMKAAAGAGYATATDLADWLVKAlGLPFREAHHVTGRLVAAASAQDKGLEELALAEMQAVEP 417
                                               ********************************************************************* PP

                                 TIGR00838 414 kleedvlevldleeavekrdakGGtakeevekaie 448
                                               +++  v+ vl +e++v+ r+++GGta+++v ++ e
  lcl|NCBI__GCF_000021745.1:WP_012590227.1 418 RINAGVFAVLGVENSVRSRMSYGGTAPANVSEQAE 452
                                               *****************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (466 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: 7.17
//
[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