Aligments for a candidate for argH in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Aligments for a candidate for argH in Dyella japonica UNC79MFTsu3.2

Align Argininosuccinate lyase; ASAL; EC 4.3.2.1; Arginosuccinase (uncharacterized)
to candidate N515DRAFT_3770 N515DRAFT_3770 argininosuccinate lyase

Query= curated2:Q4UVI4
         (431 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3770
          Length = 433

 Score =  597 bits (1540), Expect = e-175
 Identities = 302/430 (70%), Positives = 351/430 (81%), Gaps = 1/430 (0%)

Query: 1   MTNLLWQKPGVAVDAKIQTFLAGDDVILDREFFLYDIAASKAHAQGLQHIGILSLEELGG 60
           MT  LWQK G+ +DA+I  FLAGDDV+LDREFFL+DI ASKAH +GL  IG++S +E   
Sbjct: 1   MTQPLWQKSGIQIDARIMRFLAGDDVVLDREFFLHDITASKAHVEGLAKIGVVSADEAAA 60

Query: 61  LSEQLDLLADDFRSGAFVLDAHYEDCHSAIEARLTECLGDAGRKIHTGRSRNDQILVATR 120
           L  +LD LA DF +G FVLD  YED HSAIEARLTE LGDAGR++HTGRSRNDQILVATR
Sbjct: 61  LKRELDALAADFSAGDFVLDESYEDGHSAIEARLTERLGDAGRRVHTGRSRNDQILVATR 120

Query: 121 LWLKDKLQRVAALSTEVAKVALDRAQAEAELPVPGYTHIQRAVVSSAGMWWAGWAEAFID 180
           LWLKD+L  +      +A+V L+RA A+  LP+PGYTHIQRAVVSS  MW+AG+AE FID
Sbjct: 121 LWLKDQLAVLETHCRAIAEVCLERA-AQPALPLPGYTHIQRAVVSSTAMWFAGFAEGFID 179

Query: 181 NAVRANDTFKLVDTNPLGTAAGYGVNLPLDRAHTTAELGFARLQVSPIYAQLSRGKFELA 240
           N +RA  T  L+D NPLGTAAGYGVNLPLDR HTT  LGFAR+QVSP+YAQLSRGKFE+A
Sbjct: 180 NTLRARQTAALIDCNPLGTAAGYGVNLPLDREHTTQALGFARMQVSPVYAQLSRGKFEMA 239

Query: 241 ALEALGGATLDLRRIAWDLSLFTSGEFAFVALPAQYTTGSSIMPNKRNPDVIELMRATHA 300
            LEA+  A LD+RR+AWDLSLFT+ EF FV LP++YTTGSSIMPNKRNPDV+EL+RA++A
Sbjct: 240 VLEAIAAALLDVRRLAWDLSLFTTAEFGFVKLPSEYTTGSSIMPNKRNPDVVELLRASYA 299

Query: 301 SVAAARTEIEQLLSLPSGYHRDLQSSKGAIVHGFARGLAALELLPALLANLEWRPDKLRS 360
           SVAAARTEIEQLLSLPSGY RDLQ SKG++ HG   GLAALEL+P LLA +EW    +R+
Sbjct: 300 SVAAARTEIEQLLSLPSGYQRDLQFSKGSLFHGCRHGLAALELVPDLLARMEWHEPAMRA 359

Query: 361 AIDSGMYATDVAVEAAVAGVPFRDAYKAAAAASDSAGQGRTPEGSLAARVSPGAAADLQL 420
           AI+  MYATDVA+E A AGVPFRDAY+AAA A+ SAG GRTPEGSLAARVSPGA  DL+L
Sbjct: 360 AIEPAMYATDVAIEQAAAGVPFRDAYRAAADAAASAGAGRTPEGSLAARVSPGAGHDLRL 419

Query: 421 DVLRARWEAL 430
           D L+AR  AL
Sbjct: 420 DELKARLAAL 429


Lambda     K      H
   0.319    0.133    0.387 

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: 554
Number of extensions: 17
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: 431
Length of database: 433
Length adjustment: 32
Effective length of query: 399
Effective length of database: 401
Effective search space:   159999
Effective search space used:   159999
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 N515DRAFT_3770 N515DRAFT_3770 (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.21858.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
      1e-87  281.0   0.0    1.3e-87  280.6   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3770  N515DRAFT_3770 argininosuccinate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3770  N515DRAFT_3770 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.6   0.0   1.3e-87   1.3e-87      20     391 ..      25     393 ..      11     402 .. 0.95

  Alignments for each domain:
  == domain 1  score: 280.6 bits;  conditional E-value: 1.3e-87
                                    TIGR00838  20 slsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelevdaeDiHlav 85 
                                                   +  D e++ +Di++s+ah++ Lak g+++++ea+ l+++L+ l+ + ++g++ l++++eD H+a+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3770  25 DVVLDREFFLHDITASKAHVEGLAKIGVVSADEAAALKRELDALAADFSAGDFVLDESYEDGHSAI 90 
                                                  56789************************************************************* PP

                                    TIGR00838  86 ErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpg 151
                                                  E++l++++g d+g+++htgrsRnDq+ +  rl+l+d++  l ++ +++ ++ +e+A++     +pg
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3770  91 EARLTERLG-DAGRRVHTGRSRNDQILVATRLWLKDQLAVLETHCRAIAEVCLERAAQP-ALPLPG 154
                                                  *********.**********************************************987.7889** PP

                                    TIGR00838 152 ytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFd 217
                                                  ytH+qrA   + a ++  +ae +  ++ R  ++   ++ +PlG++A  g+++++dre +++ LgF+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3770 155 YTHIQRAVVSSTAMWFAGFAEGFIDNTLRARQTAALIDCNPLGTAAGYGVNLPLDREHTTQALGFA 220
                                                  ****************************************************************** PP

                                    TIGR00838 218 avvensldavsdR.DfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKK 282
                                                  ++    ++a  +R  f + +l a+a + +++ rla +l lf+++Efgfv+l+ e+++gssimP K+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3770 221 RMQVSPVYAQLSRgKFEMAVLEAIAAALLDVRRLAWDLSLFTTAEFGFVKLPSEYTTGSSIMPNKR 286
                                                  **9999999766637999************************************************ PP

                                    TIGR00838 283 npDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelk 348
                                                  npDv+El+R+  + v+   t  +  l +lP+ Y++Dlq  k +lf   ++   +le+v  ll+ ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3770 287 NPDVVELLRASYASVAAARTE-IEQLLSLPSGYQRDLQFSKGSLFHGCRHGLAALELVPDLLARME 351
                                                  ***************988665.677889************************************** PP

                                    TIGR00838 349 vnkerleeaakknfalatdlAdylvrkGvPFReaheivGevva 391
                                                   ++   ++aa +  + atd+A   ++ GvPFR+a++ + +++a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3770 352 WHEPA-MRAAIEPAMYATDVAIEQAAAGVPFRDAYRAAADAAA 393
                                                  *9888.899999************************9987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (433 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: 00:00:00.02
# Mc/sec: 7.25
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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