Alignments for a candidate for argH in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Phaeobacter inhibens BS107

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate GFF334 PGA1_c03450 argininosuccinate lyase ArgH

Query= BRENDA::Q8DVX5
         (460 letters)



>FitnessBrowser__Phaeo:GFF334
          Length = 456

 Score =  416 bits (1068), Expect = e-120
 Identities = 225/454 (49%), Positives = 290/454 (63%), Gaps = 1/454 (0%)

Query: 8   LWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAATIKAGL 67
           +WGGRF AG    +E   ASI FD+++A  D+ GS AH  ML   G+I+  DA  I+ GL
Sbjct: 1   MWGGRFAAGPDAIMEAINASIGFDKRMAAQDIAGSRAHAAMLAATGVITDNDAEAIREGL 60

Query: 68  EDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMHLYLKA 127
             +L E + G  +F  + EDIHMN+E+ L   IG  AG+LHT RSRNDQVATD  L+++ 
Sbjct: 61  LTVLSEIEGGTFQFSTALEDIHMNVEARLKDIIGEPAGRLHTGRSRNDQVATDFKLWVRD 120

Query: 128 KLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTRDSERF 187
           +LD     L  L   L+  A+     +MPG+THLQ AQP+++GHH+MAY  MF RD  R 
Sbjct: 121 QLDAAESGLLALIRALLSQAEAGADWVMPGFTHLQTAQPVTWGHHMMAYVEMFGRDLSRV 180

Query: 188 IFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEFLSNAS 247
               K  + SPLGAAALAGT+FPIDREMTA  +GF  P +NSLDAVSDRDF LEFLS AS
Sbjct: 181 RDARKRMNESPLGAAALAGTSFPIDREMTASALGFDRPAANSLDAVSDRDFALEFLSVAS 240

Query: 248 ILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGRVYANL 307
           I  +H+SR  EE++ W S +++FVTLSD FSTGSSIMPQKKNPD AELIR K GR++   
Sbjct: 241 ISAVHLSRFAEELVIWSSAQFRFVTLSDRFSTGSSIMPQKKNPDAAELIRAKVGRIFGAN 300

Query: 308 FGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAESTQKD 367
             L+ VMK LPLAY+KD+QEDKE +FD A+   +AL  + GM+  M  N   +A +    
Sbjct: 301 TALMMVMKGLPLAYSKDMQEDKEQVFDAADNWMLALAAMEGMVKDMTGNRAELAAAAGSG 360

Query: 368 FSNATELADYLAS-KGMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLIEEDVY 426
           FS AT+LAD++     +PFR AH + G L+      G  L D+ L   Q + + I ED++
Sbjct: 361 FSTATDLADWMVRVLKVPFRDAHHVTGTLVAMAESRGCDLPDLTLADMQGVHEGITEDIF 420

Query: 427 ETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKAL 460
             L    +V  R S GGT   QV+ QIA  +  L
Sbjct: 421 SVLGVENSVNSRMSYGGTAPAQVRAQIARWQDVL 454


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: 564
Number of extensions: 22
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: 460
Length of database: 456
Length adjustment: 33
Effective length of query: 427
Effective length of database: 423
Effective search space:   180621
Effective search space used:   180621
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 GFF334 PGA1_c03450 (argininosuccinate lyase ArgH)
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.3038.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   9.2e-185  600.9   0.0     1e-184  600.7   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF334  PGA1_c03450 argininosuccinate ly


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF334  PGA1_c03450 argininosuccinate lyase ArgH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.7   0.0    1e-184    1e-184       1     452 [.       1     452 [.       1     455 [. 0.99

  Alignments for each domain:
  == domain 1  score: 600.7 bits;  conditional E-value: 1e-184
                         TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelevd 77 
                                       +wggR++ ++d  +++ nas+ fDk++a++Di gs ah+++La +g++t+++a+ ++e+L ++ +e++ g++++++ 
  lcl|FitnessBrowser__Phaeo:GFF334   1 MWGGRFAAGPDAIMEAINASIGFDKRMAAQDIAGSRAHAAMLAATGVITDNDAEAIREGLLTVLSEIEGGTFQFSTA 77 
                                       6**************************************************************************** PP

                         TIGR00838  78 aeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgytH 154
                                        eDiH++vE++l d +ge +g +lhtgrsRnDqvatd++l++rd+++   + l++l++al+ +Ae+  + +mpg+tH
  lcl|FitnessBrowser__Phaeo:GFF334  78 LEDIHMNVEARLKDIIGEPAG-RLHTGRSRNDQVATDFKLWVRDQLDAAESGLLALIRALLSQAEAGADWVMPGFTH 153
                                       *****************7766.******************************************************* PP

                         TIGR00838 155 LqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdRD 231
                                       Lq AqP+t++Hh++ay+em+ rDl+R+ da kR+n+sPlG++Alagtsf+idre++a+ LgFd+ ++nsldavsdRD
  lcl|FitnessBrowser__Phaeo:GFF334 154 LQTAQPVTWGHHMMAYVEMFGRDLSRVRDARKRMNESPLGAAALAGTSFPIDREMTASALGFDRPAANSLDAVSDRD 230
                                       ***************************************************************************** PP

                         TIGR00838 232 fiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltglltil 308
                                       f++E+ls+a++ +vhlsr+aEel+++ss+ f fv+lsd++s+gssimPqKKnpD+aEliR+k gr++G  t+l++++
  lcl|FitnessBrowser__Phaeo:GFF334 231 FALEFLSVASISAVHLSRFAEELVIWSSAQFRFVTLSDRFSTGSSIMPQKKNPDAAELIRAKVGRIFGANTALMMVM 307
                                       ***************************************************************************** PP

                         TIGR00838 309 KalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrk.GvPFReahe 384
                                       K+lPlaY kD+qEdke++fda +++  +l +++g++k+++ n+ +l+ aa ++f++atdlAd++vr   vPFR+ah+
  lcl|FitnessBrowser__Phaeo:GFF334 308 KGLPLAYSKDMQEDKEQVFDAADNWMLALAAMEGMVKDMTGNRAELAAAAGSGFSTATDLADWMVRVlKVPFRDAHH 384
                                       ******************************************************************99********* PP

                         TIGR00838 385 ivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieeaka 452
                                       ++G +va a+ +G +l +ltl+ +q ++e ++ed+++vl +e++v+ r+++GGta+++v+ +i+  + 
  lcl|FitnessBrowser__Phaeo:GFF334 385 VTGTLVAMAESRGCDLPDLTLADMQGVHEGITEDIFSVLGVENSVNSRMSYGGTAPAQVRAQIARWQD 452
                                       ***************************************************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (456 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: 8.18
//
[ok]

This GapMind analysis is from Apr 09 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