Alignments for a candidate for aspA in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for aspA in Dechlorosoma suillum PS

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate Dsui_3481 Dsui_3481 aspartate ammonia-lyase

Query= BRENDA::Q0PC50
         (468 letters)



>FitnessBrowser__PS:Dsui_3481
          Length = 472

 Score =  570 bits (1469), Expect = e-167
 Identities = 285/459 (62%), Positives = 352/459 (76%)

Query: 4   RKEHDFIGELEISDEVYYGVQTFRAVENFDISHDRLKDFPRFVRALARVKKAAAMANHEL 63
           R EHD +G+ ++  E YYGV T RAVENF I+   +  +P  +RALA++K AAA AN +L
Sbjct: 6   RVEHDLLGDRKVPAEAYYGVHTLRAVENFPITGTPISIYPDLIRALAQIKLAAAKANEQL 65

Query: 64  GLLDKNIQDAIIKACDKILEGGYYDQFVVDMIQGGAGTSTNMNANEVIANIGLELMGHKK 123
           GLL+  +  AI+ AC +++ G  ++QFVVD+IQGGAGTSTNMNANEVIAN  LE+MGH K
Sbjct: 66  GLLEAPLAQAIVAACQEVIAGKLHEQFVVDVIQGGAGTSTNMNANEVIANRALEIMGHAK 125

Query: 124 GEYQYLHPNDHVNLSQSTNDAYPTALHLALHDYLSDLAKAMEHLKKAYERKAEEFKDVLK 183
           GEYQ+LHPN HVN+SQSTND YP+AL LA +  +  L  A+ +L++ +ERKAEEFKDVLK
Sbjct: 126 GEYQHLHPNQHVNMSQSTNDVYPSALKLATYVGIFRLVDALAYLRRTFERKAEEFKDVLK 185

Query: 184 MGRTQLQDAVPMTLGREFKTFAVMIGEDIQRVLEARKLILEINLGGTAIGTGINSHPDYP 243
           MGRTQLQDAVPMTLG+EF T+AVM+GED +R+ EA  LI EINLG TAIGTGIN+HPDY 
Sbjct: 186 MGRTQLQDAVPMTLGQEFSTYAVMLGEDEERLKEAALLIREINLGATAIGTGINAHPDYA 245

Query: 244 KVVERKIREVTGFEYTVAEDLIEATQDTGAYVQISGVLKRVATKLSKVCNDLRLLSSGPK 303
            +V R + E +G     A +L+EATQD G++VQ+SGVLKRVA KLSK CNDLRLLSSGP+
Sbjct: 246 PLVCRLLAETSGVPVITAPNLVEATQDCGSFVQLSGVLKRVAVKLSKTCNDLRLLSSGPR 305

Query: 304 CGLNEINLPKMQPGSSIMPGKVNPVIPEVVNQVCYFVIGADVTVTFACEGGQLQLNVFEP 363
            G  EINLP  Q GSSIMPGKVNPVIPEVVNQ+ + VIG D TVTFA E GQLQLN FEP
Sbjct: 306 AGFGEINLPPRQAGSSIMPGKVNPVIPEVVNQIAFEVIGNDQTVTFAAEAGQLQLNAFEP 365

Query: 364 VVAYSLFNSVVMLEKAMYTLADKCIDGITANEKICSDFVYNSVGIVTALNPYIGYENSAS 423
           ++A+SLF SV  L +   TLAD+C+DGITAN       V NS+GIVTALNPYIGY  + S
Sbjct: 366 IIAHSLFKSVNHLRQGCLTLADRCVDGITANRDALRARVENSIGIVTALNPYIGYAAATS 425

Query: 424 IAKEAMNTGKRVADIALERGLLSKEQIDEILTPSNMLNP 462
           +A EA+ +GK VA+I L RGL+S+ ++D++L P  +  P
Sbjct: 426 VAAEALESGKGVAEIVLARGLMSRAELDDVLRPEVLTQP 464


Lambda     K      H
   0.318    0.135    0.383 

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: 591
Number of extensions: 16
Number of successful extensions: 1
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: 468
Length of database: 472
Length adjustment: 33
Effective length of query: 435
Effective length of database: 439
Effective search space:   190965
Effective search space used:   190965
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 Dsui_3481 Dsui_3481 (aspartate ammonia-lyase)
to HMM TIGR00839 (aspA: aspartate ammonia-lyase (EC 4.3.1.1))

# 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.carbon/TIGR00839.hmm
# target sequence database:        /tmp/gapView.833.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00839  [M=468]
Accession:   TIGR00839
Description: aspA: aspartate ammonia-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.1e-223  729.3   0.0   1.2e-223  729.1   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_3481  Dsui_3481 aspartate ammonia-lyas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_3481  Dsui_3481 aspartate ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  729.1   0.0  1.2e-223  1.2e-223       1     460 [.       6     465 ..       6     471 .. 0.99

  Alignments for each domain:
  == domain 1  score: 729.1 bits;  conditional E-value: 1.2e-223
                         TIGR00839   1 riekdllGekeveaevyyGiqtlrasenfaisnekisdvpefvkalvlvkkaaalanvelkaidekiakaivaacde 77 
                                       r+e+dllG+++v+ae+yyG++tlra+enf+i+++ is +p++++al+++k aaa an +l++++  +a+aivaac+e
  lcl|FitnessBrowser__PS:Dsui_3481   6 RVEHDLLGDRKVPAEAYYGVHTLRAVENFPITGTPISIYPDLIRALAQIKLAAAKANEQLGLLEAPLAQAIVAACQE 82 
                                       89*************************************************************************** PP

                         TIGR00839  78 ileGkyldqfivdviqGGaGtsvnmntnevianlalellGhkkGeyqflnpndhvnksqstndayptalkiavyesl 154
                                       ++ Gk+++qf+vdviqGGaGts+nmn+nevian+ale++Gh kGeyq+l+pn+hvn+sqstnd+yp+alk+a+y  +
  lcl|FitnessBrowser__PS:Dsui_3481  83 VIAGKLHEQFVVDVIQGGAGTSTNMNANEVIANRALEIMGHAKGEYQHLHPNQHVNMSQSTNDVYPSALKLATYVGI 159
                                       ***************************************************************************** PP

                         TIGR00839 155 eklvdkiealrdafeqkakefadvlkmGrtqlqdavpltlGqefeayalllerdvkrikrtrelllevnlGataiGt 231
                                        +lvd++ +lr +fe+ka+ef+dvlkmGrtqlqdavp+tlGqef +ya++l +d +r+k+++ l++e+nlGataiGt
  lcl|FitnessBrowser__PS:Dsui_3481 160 FRLVDALAYLRRTFERKAEEFKDVLKMGRTQLQDAVPMTLGQEFSTYAVMLGEDEERLKEAALLIREINLGATAIGT 236
                                       ***************************************************************************** PP

                         TIGR00839 232 GlnadkeysklvvkklaevtGlplvpaenlieatsdtgayvevsgalkriavklskvcndlrllssGpraGlneinl 308
                                       G+na+++y++lv + lae +G+p+++a nl+eat+d+g++v++sg+lkr+avklsk cndlrllssGpraG+ einl
  lcl|FitnessBrowser__PS:Dsui_3481 237 GINAHPDYAPLVCRLLAETSGVPVITAPNLVEATQDCGSFVQLSGVLKRVAVKLSKTCNDLRLLSSGPRAGFGEINL 313
                                       ***************************************************************************** PP

                         TIGR00839 309 pelqaGssimpakvnpvvpevvnqvcfkviGndttvtlaaeaGqlqlnvlepviafallesisiltnaiesltdkcv 385
                                       p +qaGssimp+kvnpv+pevvnq++f+viGnd+tvt+aaeaGqlqln +ep+ia++l++s++ l +++ +l d+cv
  lcl|FitnessBrowser__PS:Dsui_3481 314 PPRQAGSSIMPGKVNPVIPEVVNQIAFEVIGNDQTVTFAAEAGQLQLNAFEPIIAHSLFKSVNHLRQGCLTLADRCV 390
                                       ***************************************************************************** PP

                         TIGR00839 386 eGitanekicedyvfnsiGivtalnpfiGyekaalvakeaiktgksvrdvvlekdllteeelddilsvenllkpa 460
                                       +Gitan++ ++  v+nsiGivtalnp+iGy +a  va ea+++gk+v ++vl ++l++++eldd+l++e l++p 
  lcl|FitnessBrowser__PS:Dsui_3481 391 DGITANRDALRARVENSIGIVTALNPYIGYAAATSVAAEALESGKGVAEIVLARGLMSRAELDDVLRPEVLTQPR 465
                                       *************************************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (472 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: 12.34
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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
the source code
instructions for running GapMind on your computer

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 catabolism of small carbon sources