Alignments for a candidate for aspA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for aspA in Cupriavidus basilensis 4G11

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate RR42_RS26135 RR42_RS26135 aspartate ammonia-lyase

Query= BRENDA::Q0PC50
         (468 letters)



>FitnessBrowser__Cup4G11:RR42_RS26135
          Length = 475

 Score =  578 bits (1490), Expect = e-169
 Identities = 288/459 (62%), Positives = 359/459 (78%)

Query: 4   RKEHDFIGELEISDEVYYGVQTFRAVENFDISHDRLKDFPRFVRALARVKKAAAMANHEL 63
           R EHD +G+ E+  +VYYGV T RAVENF I+   +  +P  ++ALA +K+AAA+ANHEL
Sbjct: 7   RTEHDLLGDCEVPADVYYGVHTLRAVENFPITGTPISIYPELIKALAYIKQAAALANHEL 66

Query: 64  GLLDKNIQDAIIKACDKILEGGYYDQFVVDMIQGGAGTSTNMNANEVIANIGLELMGHKK 123
           GLLD+   DAI+ AC ++L G  +DQFVVD+IQGGAGTSTNMNANEVIAN  LELMGH K
Sbjct: 67  GLLDEPRCDAIVAACAELLGGKLHDQFVVDVIQGGAGTSTNMNANEVIANRALELMGHNK 126

Query: 124 GEYQYLHPNDHVNLSQSTNDAYPTALHLALHDYLSDLAKAMEHLKKAYERKAEEFKDVLK 183
           GEYQYLHPN+ VN+ QSTND YP+AL +A    +  L  AM  L++A+ERKAEEF  VLK
Sbjct: 127 GEYQYLHPNEQVNIGQSTNDVYPSALKVATWFGILGLVDAMGVLRRAFERKAEEFSHVLK 186

Query: 184 MGRTQLQDAVPMTLGREFKTFAVMIGEDIQRVLEARKLILEINLGGTAIGTGINSHPDYP 243
           MGRTQLQDAVPMTLG+EF T+AVM+GED +R+ EA  LI EIN+G TAIGTGI +HPDY 
Sbjct: 187 MGRTQLQDAVPMTLGQEFSTYAVMLGEDEERLREAALLICEINMGATAIGTGITAHPDYA 246

Query: 244 KVVERKIREVTGFEYTVAEDLIEATQDTGAYVQISGVLKRVATKLSKVCNDLRLLSSGPK 303
            ++ ++++E+TG     A +LIEATQD GA+VQ+SGVLKRVA KLSK CNDLRLLSSGP+
Sbjct: 247 PLILKRLKEITGIPLMTAPNLIEATQDCGAFVQLSGVLKRVAVKLSKTCNDLRLLSSGPR 306

Query: 304 CGLNEINLPKMQPGSSIMPGKVNPVIPEVVNQVCYFVIGADVTVTFACEGGQLQLNVFEP 363
            GL EINLP MQ GSSIMPGKVNPVIPEVVNQ+ + VIG D+TV+FA E GQLQLN FEP
Sbjct: 307 AGLGEINLPAMQAGSSIMPGKVNPVIPEVVNQIAFEVIGNDITVSFAAEAGQLQLNAFEP 366

Query: 364 VVAYSLFNSVVMLEKAMYTLADKCIDGITANEKICSDFVYNSVGIVTALNPYIGYENSAS 423
           ++A+SLF SV  L     TLA++C++GITANE+     V NS+GIVTALNPYIGY N+ +
Sbjct: 367 IIAHSLFKSVSHLRNGCLTLAERCVNGITANEERLRATVENSIGIVTALNPYIGYANATA 426

Query: 424 IAKEAMNTGKRVADIALERGLLSKEQIDEILTPSNMLNP 462
           +A+EA  TG  V +I L++GLL+++++D+IL P  +  P
Sbjct: 427 VAQEAHATGGSVYEIVLQKGLLTRDELDQILRPEVLTQP 465


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: 629
Number of extensions: 11
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: 475
Length adjustment: 33
Effective length of query: 435
Effective length of database: 442
Effective search space:   192270
Effective search space used:   192270
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 RR42_RS26135 RR42_RS26135 (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.19993.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-226  737.6   0.0   3.9e-226  737.3   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS26135  RR42_RS26135 aspartate ammonia-l


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS26135  RR42_RS26135 aspartate ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  737.3   0.0  3.9e-226  3.9e-226       1     460 [.       7     466 ..       7     470 .. 1.00

  Alignments for each domain:
  == domain 1  score: 737.3 bits;  conditional E-value: 3.9e-226
                                 TIGR00839   1 riekdllGekeveaevyyGiqtlrasenfaisnekisdvpefvkalvlvkkaaalanvelkaidekiak 69 
                                               r e+dllG+ ev+a+vyyG++tlra+enf+i+++ is +pe++kal+ +k+aaalan+el+++de    
  lcl|FitnessBrowser__Cup4G11:RR42_RS26135   7 RTEHDLLGDCEVPADVYYGVHTLRAVENFPITGTPISIYPELIKALAYIKQAAALANHELGLLDEPRCD 75 
                                               89******************************************************************* PP

                                 TIGR00839  70 aivaacdeileGkyldqfivdviqGGaGtsvnmntnevianlalellGhkkGeyqflnpndhvnksqst 138
                                               aivaac e+l Gk++dqf+vdviqGGaGts+nmn+nevian+alel+Gh+kGeyq+l+pn+ vn  qst
  lcl|FitnessBrowser__Cup4G11:RR42_RS26135  76 AIVAACAELLGGKLHDQFVVDVIQGGAGTSTNMNANEVIANRALELMGHNKGEYQYLHPNEQVNIGQST 144
                                               ********************************************************************* PP

                                 TIGR00839 139 ndayptalkiavyesleklvdkiealrdafeqkakefadvlkmGrtqlqdavpltlGqefeayalller 207
                                               nd+yp+alk+a++  +  lvd++  lr afe+ka+ef +vlkmGrtqlqdavp+tlGqef +ya++l +
  lcl|FitnessBrowser__Cup4G11:RR42_RS26135 145 NDVYPSALKVATWFGILGLVDAMGVLRRAFERKAEEFSHVLKMGRTQLQDAVPMTLGQEFSTYAVMLGE 213
                                               ********************************************************************* PP

                                 TIGR00839 208 dvkrikrtrelllevnlGataiGtGlnadkeysklvvkklaevtGlplvpaenlieatsdtgayvevsg 276
                                               d +r+++++ l+ e+n+GataiGtG+ a+++y++l+ k+l+e+tG+pl++a nlieat+d+ga+v++sg
  lcl|FitnessBrowser__Cup4G11:RR42_RS26135 214 DEERLREAALLICEINMGATAIGTGITAHPDYAPLILKRLKEITGIPLMTAPNLIEATQDCGAFVQLSG 282
                                               ********************************************************************* PP

                                 TIGR00839 277 alkriavklskvcndlrllssGpraGlneinlpelqaGssimpakvnpvvpevvnqvcfkviGndttvt 345
                                               +lkr+avklsk cndlrllssGpraGl einlp++qaGssimp+kvnpv+pevvnq++f+viGnd tv+
  lcl|FitnessBrowser__Cup4G11:RR42_RS26135 283 VLKRVAVKLSKTCNDLRLLSSGPRAGLGEINLPAMQAGSSIMPGKVNPVIPEVVNQIAFEVIGNDITVS 351
                                               ********************************************************************* PP

                                 TIGR00839 346 laaeaGqlqlnvlepviafallesisiltnaiesltdkcveGitanekicedyvfnsiGivtalnpfiG 414
                                               +aaeaGqlqln +ep+ia++l++s+s l n++ +l ++cv+Gitane++++  v+nsiGivtalnp+iG
  lcl|FitnessBrowser__Cup4G11:RR42_RS26135 352 FAAEAGQLQLNAFEPIIAHSLFKSVSHLRNGCLTLAERCVNGITANEERLRATVENSIGIVTALNPYIG 420
                                               ********************************************************************* PP

                                 TIGR00839 415 yekaalvakeaiktgksvrdvvlekdllteeelddilsvenllkpa 460
                                               y +a  va+ea  tg sv+++vl+k+llt++eld+il++e l++p+
  lcl|FitnessBrowser__Cup4G11:RR42_RS26135 421 YANATAVAQEAHATGGSVYEIVLQKGLLTRDELDQILRPEVLTQPT 466
                                               ********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (475 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.65
//
[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