Alignments for a candidate for argH in Methylosarcina fibrata AML-C10

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Methylosarcina fibrata AML-C10

Align Argininosuccinate lyase; ASAL; ASL; Arginosuccinase; EC 4.3.2.1 (characterized)
to candidate WP_020564313.1 A3OW_RS0115235 argininosuccinate lyase

Query= SwissProt::Q9LAE5
         (461 letters)



>NCBI__GCF_000372865.1:WP_020564313.1
          Length = 462

 Score =  440 bits (1131), Expect = e-128
 Identities = 230/453 (50%), Positives = 306/453 (67%), Gaps = 1/453 (0%)

Query: 4   EQTWSQRFESALHPAIARFNASIGFDIELIEYDLTGSQAHAKMLAHTGIISSEEGEQLVA 63
           E+  S RF  A    +  F AS+ FD  +   D+ GS AHA ML   GI++  E + +V 
Sbjct: 7   EKLSSARFAEATDAFVEVFTASVTFDQRMAMQDIEGSLAHAAMLKECGILTETEFQDIVR 66

Query: 64  GLEQIRQEHRQGKFHPGVDAEDVHFAVEKRLTEIVGDVGKKLHTARSRNDQVGTDTRLYL 123
           GL +I Q+   G+F   +  EDVH  +E RLT+++G  GKKLHT RSRNDQV TD RLYL
Sbjct: 67  GLTEIGQDILDGRFDWSIKQEDVHMNIEARLTDLIGVAGKKLHTGRSRNDQVATDIRLYL 126

Query: 124 RDQIQQIKSELREFQGVLLDIAEKHVETLIPGYTHLQRAQPVSLAHHLLAYFQMAQRDWE 183
           R +I++I  +L   Q  +LD AE+H +T++PG+THLQ AQP++  HHL+A+F+M  RD E
Sbjct: 127 RSEIREITRQLTRLQTAVLDQAERHADTIMPGFTHLQVAQPITFGHHLMAWFEMLARDRE 186

Query: 184 RLGDVSRRVNISPLGCGALAGTTFPIDRHYTAKLLDFDNIYANSLDGVSDRDFAIEFLCA 243
           RL D ++R+N+ PLG  ALAGT++PIDR  TA+LL F    ANSLD VSDRDFAIEF   
Sbjct: 187 RLQDCNKRLNVMPLGAAALAGTSYPIDRELTAELLGFSRPSANSLDSVSDRDFAIEFTAT 246

Query: 244 ASLIMVHLSRLAEEVILWSSEEFRFVILKDSCATGSSIMPQKKNPDVPELVRGKTGRVFG 303
           ASLIM+HLSR +EE+ILWSS +F F+ + D+  TGSSIMPQKKNPDVPELVRGK GRV G
Sbjct: 247 ASLIMMHLSRFSEELILWSSAQFDFIDIPDAFCTGSSIMPQKKNPDVPELVRGKAGRVTG 306

Query: 304 HLQAMLVIMKGLPLAYNKDLQEDKEGLFDSVNTVKASLEAMTILLREGLEFRTQRLAQAV 363
           HL ++L++MK  PLAYNKD QEDKE LFD+V+T+   L A   ++   +  +  R+ QA 
Sbjct: 307 HLVSLLMLMKSQPLAYNKDNQEDKEPLFDTVDTLINCLRAYADMVPR-IGAKKDRMYQAA 365

Query: 364 TEDFSNATDVADYLAARGVPFREAYNLVGKVVKTSIAAGKLLKDLELEEWQQLHPAFAAD 423
              F+ ATD+ADYL  +G+ FR+A+  VG  V+  I  G+ L +L L E Q   P   AD
Sbjct: 366 KRGFATATDLADYLVRKGMAFRDAHEAVGLAVRLGIDTGRDLSELTLAELQAFSPLIEAD 425

Query: 424 IYEAISPRQVVAARNSHGGTGFVQVSKALIAAR 456
           ++++++    V+AR+  GGT    V KA+ AAR
Sbjct: 426 VFDSLTLEGSVSARSHVGGTAPDTVRKAVRAAR 458


Lambda     K      H
   0.320    0.135    0.384 

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: 477
Number of extensions: 14
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: 461
Length of database: 462
Length adjustment: 33
Effective length of query: 428
Effective length of database: 429
Effective search space:   183612
Effective search space used:   183612
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_020564313.1 A3OW_RS0115235 (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.7450.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.4e-194  631.3   0.2   6.1e-194  631.1   0.2    1.0  1  lcl|NCBI__GCF_000372865.1:WP_020564313.1  A3OW_RS0115235 argininosuccinate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000372865.1:WP_020564313.1  A3OW_RS0115235 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  631.1   0.2  6.1e-194  6.1e-194       3     454 ..      11     461 ..       9     462 .] 0.99

  Alignments for each domain:
  == domain 1  score: 631.1 bits;  conditional E-value: 6.1e-194
                                 TIGR00838   3 ggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegk 71 
                                               + R+++++d  v+ f+as++fD+++a +Diegs+ah+++L+++gilte+e ++++++L+e+ +++ +g+
  lcl|NCBI__GCF_000372865.1:WP_020564313.1  11 SARFAEATDAFVEVFTASVTFDQRMAMQDIEGSLAHAAMLKECGILTETEFQDIVRGLTEIGQDILDGR 79 
                                               78******************************************************************* PP

                                 TIGR00838  72 lelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvek 140
                                               ++++ ++eD+H+++E++l+d +g  +gkklhtgrsRnDqvatd+rlylr +++e++++l  l++a++++
  lcl|NCBI__GCF_000372865.1:WP_020564313.1  80 FDWSIKQEDVHMNIEARLTDLIG-VAGKKLHTGRSRNDQVATDIRLYLRSEIREITRQLTRLQTAVLDQ 147
                                               ***********************.99******************************************* PP

                                 TIGR00838 141 AekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrel 209
                                               Ae++ +t+mpg+tHLq AqPit++Hhl+a++eml+rD eRl+d  kR+n+ PlG++Alagts++idrel
  lcl|NCBI__GCF_000372865.1:WP_020564313.1 148 AERHADTIMPGFTHLQVAQPITFGHHLMAWFEMLARDRERLQDCNKRLNVMPLGAAALAGTSYPIDREL 216
                                               ********************************************************************* PP

                                 TIGR00838 210 laelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssim 278
                                               +aelLgF++  +nsld+vsdRDf+iE+ ++a+l+m+hlsr++Eelil+ss+ f+f++++d++++gssim
  lcl|NCBI__GCF_000372865.1:WP_020564313.1 217 TAELLGFSRPSANSLDSVSDRDFAIEFTATASLIMMHLSRFSEELILWSSAQFDFIDIPDAFCTGSSIM 285
                                               ********************************************************************* PP

                                 TIGR00838 279 PqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkel 347
                                               PqKKnpDv El+Rgk+grv+G+l++ll+++K++PlaYnkD qEdke+lfd+++t+ ++l++ + ++  +
  lcl|NCBI__GCF_000372865.1:WP_020564313.1 286 PQKKNPDVPELVRGKAGRVTGHLVSLLMLMKSQPLAYNKDNQEDKEPLFDTVDTLINCLRAYADMVPRI 354
                                               ********************************************************************* PP

                                 TIGR00838 348 kvnkerleeaakknfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekle 416
                                                 +k+r+ +aak++fa+atdlAdylvrkG+ FR+ahe vG +v+  i++G +l+eltl+elq++s+ +e
  lcl|NCBI__GCF_000372865.1:WP_020564313.1 355 GAKKDRMYQAAKRGFATATDLADYLVRKGMAFRDAHEAVGLAVRLGIDTGRDLSELTLAELQAFSPLIE 423
                                               ********************************************************************* PP

                                 TIGR00838 417 edvlevldleeavekrdakGGtakeevekaieeakael 454
                                                dv++ l+le +v++r+  GGta+++v+ka+ +a++ l
  lcl|NCBI__GCF_000372865.1:WP_020564313.1 424 ADVFDSLTLEGSVSARSHVGGTAPDTVRKAVRAARQAL 461
                                               ********************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (462 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.87
//
[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