Alignments for a candidate for argH in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Dinoroseobacter shibae DFL-12

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate 3609679 Dshi_3062 argininosuccinate lyase (RefSeq)

Query= BRENDA::Q8DVX5
         (460 letters)



>FitnessBrowser__Dino:3609679
          Length = 463

 Score =  438 bits (1127), Expect = e-127
 Identities = 232/459 (50%), Positives = 301/459 (65%), Gaps = 1/459 (0%)

Query: 3   TKNHKLWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAAT 62
           TK++ +WGGRF AG    +E   ASI FD++LA  D+ GS AH  ML ++GI+S +DA  
Sbjct: 4   TKSNAMWGGRFAAGPDAIMEAINASIGFDRRLARQDIDGSRAHAAMLAQQGILSSKDAEA 63

Query: 63  IKAGLEDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMH 122
           I+ GL  +L E + GQ  F  + EDIHMN+E+ L   IG  AG+LHT RSRNDQVATD  
Sbjct: 64  IREGLLTVLSEIETGQFAFSAALEDIHMNVEARLKELIGEPAGRLHTGRSRNDQVATDFK 123

Query: 123 LYLKAKLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTR 182
           L+++ +LD     L  L   L+  A+     +MPG+THLQ AQP+++GHH+MAY  MF R
Sbjct: 124 LWVRDQLDAADAGLLALLRALLAQAEAGADWVMPGFTHLQTAQPVTWGHHMMAYVEMFAR 183

Query: 183 DSERFIFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEF 242
           D  R        +  PLGAAALAGT+FP+DR+ TAQ +GF  P +NSLDAVSDRDF LEF
Sbjct: 184 DRGRMQDARARMNECPLGAAALAGTSFPLDRDATAQALGFDRPAANSLDAVSDRDFALEF 243

Query: 243 LSNASILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGR 302
           L+ ASI  MH+SRM EE++ W S +++FVTLSD FSTGSSIMPQKKNPD AELIR K GR
Sbjct: 244 LAAASICAMHLSRMAEELVIWSSAQFRFVTLSDRFSTGSSIMPQKKNPDAAELIRAKIGR 303

Query: 303 VYANLFGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAE 362
           +      LLTVMK LPLAY+KD+QEDKE +FD A+T+ +AL  + GM+  M  N   + +
Sbjct: 304 IVGANVALLTVMKGLPLAYSKDMQEDKEQVFDAADTLMLALAAMEGMVRDMTANRASLED 363

Query: 363 STQKDFSNATELADYLASK-GMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLI 421
           +    FS AT+LAD+L  +  +PFR AH + G L+      G  L D+ L   Q++   I
Sbjct: 364 AAASGFSTATDLADWLVRELNLPFRDAHHVTGTLVAMAEAKGCDLPDLSLAEMQSVHGAI 423

Query: 422 EEDVYETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKAL 460
             DV+E L  H +V  R S GGT   QV+ Q+A  K+ L
Sbjct: 424 RADVFEVLGVHNSVASRTSYGGTAPSQVRAQVARWKERL 462


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: 558
Number of extensions: 20
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: 460
Length of database: 463
Length adjustment: 33
Effective length of query: 427
Effective length of database: 430
Effective search space:   183610
Effective search space used:   183610
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 3609679 Dshi_3062 (argininosuccinate lyase (RefSeq))
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.28360.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.3e-184  599.6   0.1   2.6e-184  599.4   0.1    1.0  1  lcl|FitnessBrowser__Dino:3609679  Dshi_3062 argininosuccinate lyas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609679  Dshi_3062 argininosuccinate lyase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  599.4   0.1  2.6e-184  2.6e-184       1     454 [.       9     462 ..       9     463 .] 0.99

  Alignments for each domain:
  == domain 1  score: 599.4 bits;  conditional E-value: 2.6e-184
                         TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelevd 77 
                                       +wggR++ ++d  +++ nas+ fD +la++Di+gs ah+++La++gil++++a+ ++e+L ++ +e++ g++ ++  
  lcl|FitnessBrowser__Dino:3609679   9 MWGGRFAAGPDAIMEAINASIGFDRRLARQDIDGSRAHAAMLAQQGILSSKDAEAIREGLLTVLSEIETGQFAFSAA 85 
                                       6**************************************************************************** PP

                         TIGR00838  78 aeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgytH 154
                                        eDiH++vE++l + +ge +g +lhtgrsRnDqvatd++l++rd+++     l++ll+al+ +Ae+  + +mpg+tH
  lcl|FitnessBrowser__Dino:3609679  86 LEDIHMNVEARLKELIGEPAG-RLHTGRSRNDQVATDFKLWVRDQLDAADAGLLALLRALLAQAEAGADWVMPGFTH 161
                                       *****************7766.******************************************************* PP

                         TIGR00838 155 LqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdRD 231
                                       Lq AqP+t++Hh++ay+em++rD  R++da  R+n++PlG++Alagtsf++dr+++a+ LgFd+ ++nsldavsdRD
  lcl|FitnessBrowser__Dino:3609679 162 LQTAQPVTWGHHMMAYVEMFARDRGRMQDARARMNECPLGAAALAGTSFPLDRDATAQALGFDRPAANSLDAVSDRD 238
                                       ***************************************************************************** PP

                         TIGR00838 232 fiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltglltil 308
                                       f++E+l+aa+++++hlsr+aEel+++ss+ f fv+lsd++s+gssimPqKKnpD+aEliR+k gr++G  ++llt++
  lcl|FitnessBrowser__Dino:3609679 239 FALEFLAAASICAMHLSRMAEELVIWSSAQFRFVTLSDRFSTGSSIMPQKKNPDAAELIRAKIGRIVGANVALLTVM 315
                                       ***************************************************************************** PP

                         TIGR00838 309 KalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrk.GvPFReahe 384
                                       K+lPlaY kD+qEdke++fda +t+  +l +++g++++++ n+  le+aa+++f++atdlAd+lvr+  +PFR+ah+
  lcl|FitnessBrowser__Dino:3609679 316 KGLPLAYSKDMQEDKEQVFDAADTLMLALAAMEGMVRDMTANRASLEDAAASGFSTATDLADWLVRElNLPFRDAHH 392
                                       ***************************************************************************** PP

                         TIGR00838 385 ivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaieeakael 454
                                       ++G +va a++kG +l +l+l+e+q ++ +++ dv+evl ++++v+ r+++GGta+++v+ +++  k++l
  lcl|FitnessBrowser__Dino:3609679 393 VTGTLVAMAEAKGCDLPDLSLAEMQSVHGAIRADVFEVLGVHNSVASRTSYGGTAPSQVRAQVARWKERL 462
                                       *****************************************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (463 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: 00:00:00.01
# Mc/sec: 10.57
//
[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