Alignments for a candidate for patA in Escherichia coli BW25113

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.23848.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.78
//
[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