GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Escherichia coli BW25113

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 17148 b3073 putrescine:2-oxoglutaric acid aminotransferase, PLP-dependent (RefSeq)

Query= BRENDA::P42588
         (459 letters)



>FitnessBrowser__Keio:17148
          Length = 459

 Score =  909 bits (2349), Expect = 0.0
 Identities = 459/459 (100%), Positives = 459/459 (100%)

Query: 1   MNRLPSSASALACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEYRKSVTAG 60
           MNRLPSSASALACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEYRKSVTAG
Sbjct: 1   MNRLPSSASALACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEYRKSVTAG 60

Query: 61  GDYGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQE 120
           GDYGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQE
Sbjct: 61  GDYGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQE 120

Query: 121 LLDPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAF 180
           LLDPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAF
Sbjct: 121 LLDPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAF 180

Query: 181 HGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPI 240
           HGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPI
Sbjct: 181 HGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPI 240

Query: 241 QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAK 300
           QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAK
Sbjct: 241 QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAK 300

Query: 301 ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAE 360
           ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAE
Sbjct: 301 ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAE 360

Query: 361 QKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLN 420
           QKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLN
Sbjct: 361 QKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLN 420

Query: 421 NAKTIRIEPPLTLTIEQCELVIKAARKALAAMRVSVEEA 459
           NAKTIRIEPPLTLTIEQCELVIKAARKALAAMRVSVEEA
Sbjct: 421 NAKTIRIEPPLTLTIEQCELVIKAARKALAAMRVSVEEA 459


Lambda     K      H
   0.320    0.135    0.393 

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: 865
Number of extensions: 24
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: 459
Length of database: 459
Length adjustment: 33
Effective length of query: 426
Effective length of database: 426
Effective search space:   181476
Effective search space used:   181476
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate 17148 b3073 (putrescine:2-oxoglutaric acid aminotransferase, PLP-dependent (RefSeq))
to HMM TIGR03372 (ygjG: putrescine aminotransferase (EC 2.6.1.82))

# 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/TIGR03372.hmm
# target sequence database:        /tmp/gapView.377147.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03372  [M=442]
Accession:   TIGR03372
Description: putres_am_tran: putrescine aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.5e-299  977.3   1.1   5.2e-299  977.1   1.1    1.0  1  lcl|FitnessBrowser__Keio:17148  b3073 putrescine:2-oxoglutaric a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17148  b3073 putrescine:2-oxoglutaric acid aminotransferase, PLP-dependent (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  977.1   1.1  5.2e-299  5.2e-299       1     442 []       8     449 ..       8     449 .. 1.00

  Alignments for each domain:
  == domain 1  score: 977.1 bits;  conditional E-value: 5.2e-299
                       TIGR03372   1 lsalecsaqalnliekdtldheemkalnrevleyfkeyvnpgfleyrksvtaggdygavewrasglntlvdtqgqeyld 79 
                                     +sal+csa+alnliek+tldheemkalnrev+eyfke+vnpgfleyrksvtaggdygavew+a+ lntlvdtqgqe++d
  lcl|FitnessBrowser__Keio:17148   8 ASALACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEYRKSVTAGGDYGAVEWQAGSLNTLVDTQGQEFID 86 
                                     589**************************************************************************** PP

                       TIGR03372  80 clggygifnvghrnpvvvaavesqlakqplhsqelldplrallaktlaaltpgklkysffsnsgtesveaalklakayq 158
                                     clgg+gifnvghrnpvvv+av++qlakqplhsqelldplra+laktlaaltpgklkysff+nsgtesveaalklakayq
  lcl|FitnessBrowser__Keio:17148  87 CLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQ 165
                                     ******************************************************************************* PP

                       TIGR03372 159 sprgkytfiaasgafhgkslgalsataksafrkpfmpllpgfrhvafgdieamlkalqeckktgddvaavilepiqgeg 237
                                     sprgk+tfia+sgafhgkslgalsataks+frkpfmpllpgfrhv+fg+ieam++al+eckktgddvaavilepiqgeg
  lcl|FitnessBrowser__Keio:17148 166 SPRGKFTFIATSGAFHGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEG 244
                                     ******************************************************************************* PP

                       TIGR03372 238 gvilppenyltavrklcdevgallildevqtgmgrtgkmfacehenvqpdilclakalgggvmpigatvateevfsvlf 316
                                     gvilpp++yltavrklcde+gal+ildevqtgmgrtgkmfacehenvqpdilclakalgggvmpigat+ateevfsvlf
  lcl|FitnessBrowser__Keio:17148 245 GVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATIATEEVFSVLF 323
                                     ******************************************************************************* PP

                       TIGR03372 317 enpflhtttfggnplacaaalatvnvlleknlpeqaeikgellldglrqlaaeypdlvieargkgllqaiefvdneigy 395
                                     +npflhtttfggnplacaaalat+nvlle+nlp+qae+kg++lldg+rqla+eypdlv+eargkg+l+aiefvdneigy
  lcl|FitnessBrowser__Keio:17148 324 DNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGY 402
                                     ******************************************************************************* PP

                       TIGR03372 396 afakelfrrrvlvagtlnnaksvrieppltltieqcelvlkeakdvl 442
                                     +fa+e+fr+rvlvagtlnnak++rieppltltieqcelv+k+a+++l
  lcl|FitnessBrowser__Keio:17148 403 NFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTIEQCELVIKAARKAL 449
                                     ********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (442 nodes)
Target sequences:                          1  (459 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 29.06
//
[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