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.14740.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.41
//
[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:

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