Alignments for a candidate for odc in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for odc in Escherichia coli BW25113

Align ornithine decarboxylase, degradative (EC 4.1.1.17) (characterized)
to candidate 14824 b0693 ornithine decarboxylase isozyme, inducible (NCBI)

Query= ecocyc::ORNDECARBOXDEG-MONOMER
         (732 letters)



>FitnessBrowser__Keio:14824
          Length = 732

 Score = 1503 bits (3891), Expect = 0.0
 Identities = 732/732 (100%), Positives = 732/732 (100%)

Query: 1   MSKLKIAVSDSCPDCFTTQRECIYINESRNIDVAAIVLSLNDVTCGKLDEIDATGYGIPV 60
           MSKLKIAVSDSCPDCFTTQRECIYINESRNIDVAAIVLSLNDVTCGKLDEIDATGYGIPV
Sbjct: 1   MSKLKIAVSDSCPDCFTTQRECIYINESRNIDVAAIVLSLNDVTCGKLDEIDATGYGIPV 60

Query: 61  FIATENQERVPAEYLPRISGVFENCESRREFYGRQLETAASHYETQLRPPFFRALVDYVN 120
           FIATENQERVPAEYLPRISGVFENCESRREFYGRQLETAASHYETQLRPPFFRALVDYVN
Sbjct: 61  FIATENQERVPAEYLPRISGVFENCESRREFYGRQLETAASHYETQLRPPFFRALVDYVN 120

Query: 121 QGNSAFDCPGHQGGEFFRRHPAGNQFVEYFGEALFRADLCNADVAMGDLLIHEGAPCIAQ 180
           QGNSAFDCPGHQGGEFFRRHPAGNQFVEYFGEALFRADLCNADVAMGDLLIHEGAPCIAQ
Sbjct: 121 QGNSAFDCPGHQGGEFFRRHPAGNQFVEYFGEALFRADLCNADVAMGDLLIHEGAPCIAQ 180

Query: 181 QHAAKVFNADKTYFVLNGTSSSNKVVLNALLTPGDLVLFDRNNHKSNHHGALLQAGATPV 240
           QHAAKVFNADKTYFVLNGTSSSNKVVLNALLTPGDLVLFDRNNHKSNHHGALLQAGATPV
Sbjct: 181 QHAAKVFNADKTYFVLNGTSSSNKVVLNALLTPGDLVLFDRNNHKSNHHGALLQAGATPV 240

Query: 241 YLETARNPYGFIGGIDAHCFEESYLRELIAEVAPQRAKEARPFRLAVIQLGTYDGTIYNA 300
           YLETARNPYGFIGGIDAHCFEESYLRELIAEVAPQRAKEARPFRLAVIQLGTYDGTIYNA
Sbjct: 241 YLETARNPYGFIGGIDAHCFEESYLRELIAEVAPQRAKEARPFRLAVIQLGTYDGTIYNA 300

Query: 301 RQVVDKIGHLCDYILFDSAWVGYEQFIPMMADCSPLLLDLNENDPGILVTQSVHKQQAGF 360
           RQVVDKIGHLCDYILFDSAWVGYEQFIPMMADCSPLLLDLNENDPGILVTQSVHKQQAGF
Sbjct: 301 RQVVDKIGHLCDYILFDSAWVGYEQFIPMMADCSPLLLDLNENDPGILVTQSVHKQQAGF 360

Query: 361 SQTSQIHKKDSHIKGQQRYVPHKRMNNAFMMHASTSPFYPLFAALNINAKMHEGVSGRNM 420
           SQTSQIHKKDSHIKGQQRYVPHKRMNNAFMMHASTSPFYPLFAALNINAKMHEGVSGRNM
Sbjct: 361 SQTSQIHKKDSHIKGQQRYVPHKRMNNAFMMHASTSPFYPLFAALNINAKMHEGVSGRNM 420

Query: 421 WMDCVVNGINARKLILDNCQHIRPFVPELVDGKPWQSYETAQIAVDLRFFQFVPGEHWHS 480
           WMDCVVNGINARKLILDNCQHIRPFVPELVDGKPWQSYETAQIAVDLRFFQFVPGEHWHS
Sbjct: 421 WMDCVVNGINARKLILDNCQHIRPFVPELVDGKPWQSYETAQIAVDLRFFQFVPGEHWHS 480

Query: 481 FEGYAENQYFVDPCKLLLTTPGIDARNGEYEAFGVPATILANFLRENGVVPEKCDLNSIL 540
           FEGYAENQYFVDPCKLLLTTPGIDARNGEYEAFGVPATILANFLRENGVVPEKCDLNSIL
Sbjct: 481 FEGYAENQYFVDPCKLLLTTPGIDARNGEYEAFGVPATILANFLRENGVVPEKCDLNSIL 540

Query: 541 FLLTPAEDMAKLQQLVALLVRFEKLLESDAPLAEVLPSIYKQHEERYAGYTLRQLCQEMH 600
           FLLTPAEDMAKLQQLVALLVRFEKLLESDAPLAEVLPSIYKQHEERYAGYTLRQLCQEMH
Sbjct: 541 FLLTPAEDMAKLQQLVALLVRFEKLLESDAPLAEVLPSIYKQHEERYAGYTLRQLCQEMH 600

Query: 601 DLYARHNVKQLQKEMFRKEHFPRVSMNPQEANYAYLRGEVELVRLPDAEGRIAAEGALPY 660
           DLYARHNVKQLQKEMFRKEHFPRVSMNPQEANYAYLRGEVELVRLPDAEGRIAAEGALPY
Sbjct: 601 DLYARHNVKQLQKEMFRKEHFPRVSMNPQEANYAYLRGEVELVRLPDAEGRIAAEGALPY 660

Query: 661 PPGVLCVVPGEIWGGAVLRYFSALEEGINLLPGFAPELQGVYIEEHDGRKQVWCYVIKPR 720
           PPGVLCVVPGEIWGGAVLRYFSALEEGINLLPGFAPELQGVYIEEHDGRKQVWCYVIKPR
Sbjct: 661 PPGVLCVVPGEIWGGAVLRYFSALEEGINLLPGFAPELQGVYIEEHDGRKQVWCYVIKPR 720

Query: 721 DAQSTLLKGEKL 732
           DAQSTLLKGEKL
Sbjct: 721 DAQSTLLKGEKL 732


Lambda     K      H
   0.322    0.138    0.424 

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: 2060
Number of extensions: 61
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: 732
Length of database: 732
Length adjustment: 40
Effective length of query: 692
Effective length of database: 692
Effective search space:   478864
Effective search space used:   478864
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 (21.9 bits)
S2: 55 (25.8 bits)

Align candidate 14824 b0693 (ornithine decarboxylase isozyme, inducible (NCBI))
to HMM TIGR04301 (speF: ornithine decarboxylase SpeF (EC 4.1.1.17))

# 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/TIGR04301.hmm
# target sequence database:        /tmp/gapView.26540.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR04301  [M=719]
Accession:   TIGR04301
Description: ODC_inducible: ornithine decarboxylase SpeF
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
          0 1433.6   0.0          0 1433.4   0.0    1.0  1  lcl|FitnessBrowser__Keio:14824  b0693 ornithine decarboxylase is


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14824  b0693 ornithine decarboxylase isozyme, inducible (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1433.4   0.0         0         0       1     719 []       1     718 [.       1     718 [. 1.00

  Alignments for each domain:
  == domain 1  score: 1433.4 bits;  conditional E-value: 0
                       TIGR04301   1 mkklkiavsesvkdafeterevveleetdftdvaavvlsvedvkagvlekieetafeipvfvvveeeekvsaellkkvt 79 
                                     m+klkiavs+s+ d+f+t+re++ ++e++ +dvaa+vls++dv++g+l++i++t+++ipvf+++e++e+v+ae+l++++
  lcl|FitnessBrowser__Keio:14824   1 MSKLKIAVSDSCPDCFTTQRECIYINESRNIDVAAIVLSLNDVTCGKLDEIDATGYGIPVFIATENQERVPAEYLPRIS 79 
                                     89***************************************************************************** PP

                       TIGR04301  80 gvidleekdaelygrqleeaakkyeekllppffkalkkyvekgnsafdcpghqggeffrkhpagrqfvdffgenlfrsd 158
                                     gv++++e+++e+ygrqle+aa++ye++l+ppff+al++yv++gnsafdcpghqggeffr+hpag+qfv++fge+lfr+d
  lcl|FitnessBrowser__Keio:14824  80 GVFENCESRREFYGRQLETAASHYETQLRPPFFRALVDYVNQGNSAFDCPGHQGGEFFRRHPAGNQFVEYFGEALFRAD 158
                                     ******************************************************************************* PP

                       TIGR04301 159 lcnadvalgdllihegaplaaqkhaakvfnadktyfvlngtsasnkvvlnallapgdlvlfdrnnhksnhhgallqaga 237
                                     lcnadva+gdllihegap+ aq+haakvfnadktyfvlngts+snkvvlnall+pgdlvlfdrnnhksnhhgallqaga
  lcl|FitnessBrowser__Keio:14824 159 LCNADVAMGDLLIHEGAPCIAQQHAAKVFNADKTYFVLNGTSSSNKVVLNALLTPGDLVLFDRNNHKSNHHGALLQAGA 237
                                     ******************************************************************************* PP

                       TIGR04301 238 tpvyletarnpfgfiggidehcfeeeylrelirevaperakekrpfrlaviqlgtydgtiynarqvvdkighlcdyilf 316
                                     tpvyletarnp+gfiggid+hcfee+ylreli+evap+rake+rpfrlaviqlgtydgtiynarqvvdkighlcdyilf
  lcl|FitnessBrowser__Keio:14824 238 TPVYLETARNPYGFIGGIDAHCFEESYLRELIAEVAPQRAKEARPFRLAVIQLGTYDGTIYNARQVVDKIGHLCDYILF 316
                                     ******************************************************************************* PP

                       TIGR04301 317 dsawvgyeqfipmmkdcsplllelneedpgilvtqsvhkqqagfsqtsqihkkdkhikgqaryvnhkrlnnafmlhast 395
                                     dsawvgyeqfipmm+dcsplll+lne+dpgilvtqsvhkqqagfsqtsqihkkd+hikgq+ryv+hkr+nnafm+hast
  lcl|FitnessBrowser__Keio:14824 317 DSAWVGYEQFIPMMADCSPLLLDLNENDPGILVTQSVHKQQAGFSQTSQIHKKDSHIKGQQRYVPHKRMNNAFMMHAST 395
                                     ******************************************************************************* PP

                       TIGR04301 396 spfyplfaaldvnaklhegeagkrlwadcvktgiearklllkscklikpfvpelvdgkkwedydteeiandlrffefep 474
                                     spfyplfaal++nak+heg +g+++w+dcv +gi+arkl+l++c++i+pfvpelvdgk+w++y+t++ia dlrff+f+p
  lcl|FitnessBrowser__Keio:14824 396 SPFYPLFAALNINAKMHEGVSGRNMWMDCVVNGINARKLILDNCQHIRPFVPELVDGKPWQSYETAQIAVDLRFFQFVP 474
                                     ******************************************************************************* PP

                       TIGR04301 475 gekwhsfegyeeeqyfvdpcklllttpgidvetgeyeefgvpatilanflrengiipekcdlnsilflltpaedlaklq 553
                                     ge+whsfegy+e+qyfvdpcklllttpgid+++geye fgvpatilanflreng++pekcdlnsilflltpaed+aklq
  lcl|FitnessBrowser__Keio:14824 475 GEHWHSFEGYAENQYFVDPCKLLLTTPGIDARNGEYEAFGVPATILANFLRENGVVPEKCDLNSILFLLTPAEDMAKLQ 553
                                     ******************************************************************************* PP

                       TIGR04301 554 elvaqiarfeklleedaplkevlpsvykaneerykgytirqlcqemhdlykernvkqlqkelfrkeylpkvvlnpqean 632
                                     +lva ++rfeklle+dapl+evlps+yk++eery gyt+rqlcqemhdly+++nvkqlqke+frke++p+v++npqean
  lcl|FitnessBrowser__Keio:14824 554 QLVALLVRFEKLLESDAPLAEVLPSIYKQHEERYAGYTLRQLCQEMHDLYARHNVKQLQKEMFRKEHFPRVSMNPQEAN 632
                                     ******************************************************************************* PP

                       TIGR04301 633 leflrgevelveleeaegriaaegalpyppgvlcvvpgevwggavlkyflaleeginllpgfapelqgvyleededgrk 711
                                     +++lrgevelv+l +aegriaaegalpyppgvlcvvpge+wggavl+yf aleeginllpgfapelqgvy+e ++dgrk
  lcl|FitnessBrowser__Keio:14824 633 YAYLRGEVELVRLPDAEGRIAAEGALPYPPGVLCVVPGEIWGGAVLRYFSALEEGINLLPGFAPELQGVYIE-EHDGRK 710
                                     ************************************************************************.9***** PP

                       TIGR04301 712 raygyvlk 719
                                     ++++yv+k
  lcl|FitnessBrowser__Keio:14824 711 QVWCYVIK 718
                                     ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (719 nodes)
Target sequences:                          1  (732 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 8.09
//
[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