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.17851.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: 7.26
//
[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:

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:

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:

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:

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