Alignments for a candidate for aspA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for aspA in Pseudomonas putida KT2440

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate PP_5338 PP_5338 aspartate ammonia-lyase

Query= BRENDA::Q9HTD7
         (474 letters)



>FitnessBrowser__Putida:PP_5338
          Length = 478

 Score =  831 bits (2147), Expect = 0.0
 Identities = 425/474 (89%), Positives = 444/474 (93%)

Query: 1   MSPVASSRIEKDLLGTLEVPADAYYGIQTLRAVNNFRLSGVPLSHYPKLVVALAMVKQAA 60
           MS  AS R+EKDLLGTLEVPADAYYGIQTLRA NNF LSGVPLSHYPKLVVALAMVKQAA
Sbjct: 5   MSSAASFRVEKDLLGTLEVPADAYYGIQTLRAANNFHLSGVPLSHYPKLVVALAMVKQAA 64

Query: 61  ADANRQLGHLPEDKHAAISEACARLIRGDFHEQFVVDMIQGGAGTSTNMNANEVIANIAL 120
           ADANR+LGHL + KHAAIS ACARLI+GDFH+QFVVDMIQGGAGTSTNMNANEVIAN+AL
Sbjct: 65  ADANRELGHLSDAKHAAISAACARLIKGDFHDQFVVDMIQGGAGTSTNMNANEVIANVAL 124

Query: 121 EAMGHTKGEYKYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDTLLASLDSLIQAFAAKGV 180
           EAMGH KGEY+YLHPNNDVNMAQSTNDAYPTAIRLGLLLGHD LLASLDSLIQAFAAKG 
Sbjct: 125 EAMGHQKGEYQYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDALLASLDSLIQAFAAKGK 184

Query: 181 EFAGVLKMGRTQLQDAVPMTLGQEFHAFATTLGEDLDRLRRLAPELLTEVNLGGTAIGTG 240
           EF  VLKMGRTQLQDAVPMTLGQEF AFATT+ EDL RLR LAPELLTE+NLGGTAIGTG
Sbjct: 185 EFDHVLKMGRTQLQDAVPMTLGQEFRAFATTMTEDLQRLRSLAPELLTEINLGGTAIGTG 244

Query: 241 INADPGYQKLAVERLAAISGQPLKPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL 300
           INADPGYQ LAV+RLA ISG PL PAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL
Sbjct: 245 INADPGYQALAVQRLATISGHPLVPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL 304

Query: 301 RLLSSGPRTGINEINLPPRQPGSSIMPGKVNPVIPEAVNQVAFEVIGNDLALTLAAEGGQ 360
           RLLSSGPRTGINEINLP RQPGSSIMPGKVNPVIPEAVNQVAF ++GNDLALT+AAEGGQ
Sbjct: 305 RLLSSGPRTGINEINLPARQPGSSIMPGKVNPVIPEAVNQVAFAIMGNDLALTVAAEGGQ 364

Query: 361 LQLNVMEPLIAYKIFDSIRLLQRAMDMLREHCITGITANVERCHELVEHSIGLVTALNPY 420
           LQLNVMEPLIAYKIFDSIRLLQRAMDMLREHCI GITAN +RC ELVEHSIGLVTALNPY
Sbjct: 365 LQLNVMEPLIAYKIFDSIRLLQRAMDMLREHCIVGITANEQRCRELVEHSIGLVTALNPY 424

Query: 421 IGYENSTRIAKTALESGRGVLELVREEKLLDEATLADILLPENMIAPRLIPLRA 474
           IGYEN+TRIA+ ALESGRGVLELVREEKLLD+A L DIL PENMIAPRL+PL+A
Sbjct: 425 IGYENATRIARVALESGRGVLELVREEKLLDDAMLDDILRPENMIAPRLVPLKA 478


Lambda     K      H
   0.318    0.135    0.380 

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: 810
Number of extensions: 21
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: 474
Length of database: 478
Length adjustment: 33
Effective length of query: 441
Effective length of database: 445
Effective search space:   196245
Effective search space used:   196245
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 PP_5338 PP_5338 (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.1946062.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   8.7e-213  693.3   0.1     1e-212  693.1   0.1    1.0  1  lcl|FitnessBrowser__Putida:PP_5338  PP_5338 aspartate ammonia-lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5338  PP_5338 aspartate ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  693.1   0.1    1e-212    1e-212       1     460 [.      12     472 ..      12     477 .. 0.99

  Alignments for each domain:
  == domain 1  score: 693.1 bits;  conditional E-value: 1e-212
                           TIGR00839   1 riekdllGekeveaevyyGiqtlrasenfaisnekisdvpefvkalvlvkkaaalanvelkaidekiakaivaac 75 
                                         r+ekdllG+ ev+a++yyGiqtlra++nf++s++ +s++p++v al++vk+aaa an el+++++    ai aac
  lcl|FitnessBrowser__Putida:PP_5338  12 RVEKDLLGTLEVPADAYYGIQTLRAANNFHLSGVPLSHYPKLVVALAMVKQAAADANRELGHLSDAKHAAISAAC 86 
                                         89************************************************************************* PP

                           TIGR00839  76 deileGkyldqfivdviqGGaGtsvnmntnevianlalellGhkkGeyqflnpndhvnksqstndayptalkiav 150
                                           +++G ++dqf+vd+iqGGaGts+nmn+nevian+ale +Gh+kGeyq+l+pn+ vn++qstndaypta+++ +
  lcl|FitnessBrowser__Putida:PP_5338  87 ARLIKGDFHDQFVVDMIQGGAGTSTNMNANEVIANVALEAMGHQKGEYQYLHPNNDVNMAQSTNDAYPTAIRLGL 161
                                         *************************************************************************** PP

                           TIGR00839 151 yesleklvdkiealrdafeqkakefadvlkmGrtqlqdavpltlGqefeayalllerdvkrikr.trelllevnl 224
                                         +     l++++++l +af+ k kef++vlkmGrtqlqdavp+tlGqef+a+a  + +d++r+++ + ell e+nl
  lcl|FitnessBrowser__Putida:PP_5338 162 LLGHDALLASLDSLIQAFAAKGKEFDHVLKMGRTQLQDAVPMTLGQEFRAFATTMTEDLQRLRSlAPELLTEINL 236
                                         **************************************************************98356899***** PP

                           TIGR00839 225 GataiGtGlnadkeysklvvkklaevtGlplvpaenlieatsdtgayvevsgalkriavklskvcndlrllssGp 299
                                         G+taiGtG+nad++y+ l+v++la ++G plvpa +lieatsd ga+v  sg lkr+avklsk+cndlrllssGp
  lcl|FitnessBrowser__Putida:PP_5338 237 GGTAIGTGINADPGYQALAVQRLATISGHPLVPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDLRLLSSGP 311
                                         *************************************************************************** PP

                           TIGR00839 300 raGlneinlpelqaGssimpakvnpvvpevvnqvcfkviGndttvtlaaeaGqlqlnvlepviafallesisilt 374
                                         r+G+neinlp++q+Gssimp+kvnpv+pe vnqv+f+++Gnd ++t+aae+Gqlqlnv+ep+ia+++++si +l+
  lcl|FitnessBrowser__Putida:PP_5338 312 RTGINEINLPARQPGSSIMPGKVNPVIPEAVNQVAFAIMGNDLALTVAAEGGQLQLNVMEPLIAYKIFDSIRLLQ 386
                                         *************************************************************************** PP

                           TIGR00839 375 naiesltdkcveGitanekicedyvfnsiGivtalnpfiGyekaalvakeaiktgksvrdvvlekdllteeeldd 449
                                         +a+  l+++c+ Gitane++c++ v++siG+vtalnp+iGye+a ++a++a+++g++v ++v e++ll ++ ldd
  lcl|FitnessBrowser__Putida:PP_5338 387 RAMDMLREHCIVGITANEQRCRELVEHSIGLVTALNPYIGYENATRIARVALESGRGVLELVREEKLLDDAMLDD 461
                                         *************************************************************************** PP

                           TIGR00839 450 ilsvenllkpa 460
                                         il++en++ p 
  lcl|FitnessBrowser__Putida:PP_5338 462 ILRPENMIAPR 472
                                         ********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (478 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 17.44
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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