Alignments for a candidate for sdaB in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Escherichia coli BW25113

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate 16881 b2797 L-serine deaminase II (NCBI)

Query= BRENDA::P30744
         (455 letters)



>FitnessBrowser__Keio:16881
          Length = 455

 Score =  901 bits (2328), Expect = 0.0
 Identities = 455/455 (100%), Positives = 455/455 (100%)

Query: 1   MISVFDIFKIGIGPSSSHTVGPMKAGKQFTDDLIARNLLKDVTRVVVDVYGSLSLTGKGH 60
           MISVFDIFKIGIGPSSSHTVGPMKAGKQFTDDLIARNLLKDVTRVVVDVYGSLSLTGKGH
Sbjct: 1   MISVFDIFKIGIGPSSSHTVGPMKAGKQFTDDLIARNLLKDVTRVVVDVYGSLSLTGKGH 60

Query: 61  HTDIAIIMGLAGNLPDTVDIDSIPSFIQDVNTHGRLMLANGQHEVEFPVDQCMNFHADNL 120
           HTDIAIIMGLAGNLPDTVDIDSIPSFIQDVNTHGRLMLANGQHEVEFPVDQCMNFHADNL
Sbjct: 61  HTDIAIIMGLAGNLPDTVDIDSIPSFIQDVNTHGRLMLANGQHEVEFPVDQCMNFHADNL 120

Query: 121 SLHENGMRITALAGDKVVYSQTYYSIGGGFIVDEEHFGQQDSAPVEVPYPYSSAADLQKH 180
           SLHENGMRITALAGDKVVYSQTYYSIGGGFIVDEEHFGQQDSAPVEVPYPYSSAADLQKH
Sbjct: 121 SLHENGMRITALAGDKVVYSQTYYSIGGGFIVDEEHFGQQDSAPVEVPYPYSSAADLQKH 180

Query: 181 CQETGLSLSGLMMKNELALHSKEELEQHLANVWEVMRGGIERGISTEGVLPGKLRVPRRA 240
           CQETGLSLSGLMMKNELALHSKEELEQHLANVWEVMRGGIERGISTEGVLPGKLRVPRRA
Sbjct: 181 CQETGLSLSGLMMKNELALHSKEELEQHLANVWEVMRGGIERGISTEGVLPGKLRVPRRA 240

Query: 241 AALRRMLVSQDKTTTDPMAVVDWINMFALAVNEENAAGGRVVTAPTNGACGIIPAVLAYY 300
           AALRRMLVSQDKTTTDPMAVVDWINMFALAVNEENAAGGRVVTAPTNGACGIIPAVLAYY
Sbjct: 241 AALRRMLVSQDKTTTDPMAVVDWINMFALAVNEENAAGGRVVTAPTNGACGIIPAVLAYY 300

Query: 301 DKFIREVNANSLARYLLVASAIGSLYKMNASISGAEVGCQGEVGVACSMAAAGLAELLGA 360
           DKFIREVNANSLARYLLVASAIGSLYKMNASISGAEVGCQGEVGVACSMAAAGLAELLGA
Sbjct: 301 DKFIREVNANSLARYLLVASAIGSLYKMNASISGAEVGCQGEVGVACSMAAAGLAELLGA 360

Query: 361 SPAQVCIAAEIAMEHNLGLTCDPVAGQVQVPCIERNAIAAVKAVNAARMALRRTSEPRVC 420
           SPAQVCIAAEIAMEHNLGLTCDPVAGQVQVPCIERNAIAAVKAVNAARMALRRTSEPRVC
Sbjct: 361 SPAQVCIAAEIAMEHNLGLTCDPVAGQVQVPCIERNAIAAVKAVNAARMALRRTSEPRVC 420

Query: 421 LDKVIETMYETGKDMNAKYRETSRGGLAMKIVACD 455
           LDKVIETMYETGKDMNAKYRETSRGGLAMKIVACD
Sbjct: 421 LDKVIETMYETGKDMNAKYRETSRGGLAMKIVACD 455


Lambda     K      H
   0.319    0.134    0.388 

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: 755
Number of extensions: 14
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: 455
Length of database: 455
Length adjustment: 33
Effective length of query: 422
Effective length of database: 422
Effective search space:   178084
Effective search space used:   178084
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 16881 b2797 (L-serine deaminase II (NCBI))
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))

# 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/TIGR00720.hmm
# target sequence database:        /tmp/gapView.5653.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00720  [M=450]
Accession:   TIGR00720
Description: sda_mono: L-serine 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-227  739.3   1.9   9.9e-227  739.1   1.9    1.0  1  lcl|FitnessBrowser__Keio:16881  b2797 L-serine deaminase II (NCB


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16881  b2797 L-serine deaminase II (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  739.1   1.9  9.9e-227  9.9e-227       1     450 []       2     451 ..       2     451 .. 0.99

  Alignments for each domain:
  == domain 1  score: 739.1 bits;  conditional E-value: 9.9e-227
                       TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpeevdi 79 
                                     isvfd+fkiGiGPssshtvGPmka+k+f ++l  ++ l++v+rv vd+yGsl+ltGkGh+td a+++Gl+G+lp++vdi
  lcl|FitnessBrowser__Keio:16881   2 ISVFDIFKIGIGPSSSHTVGPMKAGKQFTDDLIARNLLKDVTRVVVDVYGSLSLTGKGHHTDIAIIMGLAGNLPDTVDI 80 
                                     79***************************************************************************** PP

                       TIGR00720  80 esieklleeveeekklkla.nqkeikfdlekdlafkdevlplhenglrlkaydeegevlkektyysvGGGfivdeeelk 157
                                     +si++++++v+++++l la +q+e++f +++ ++f+ ++l+lheng+r++a++++ +v++++tyys+GGGfivdee+++
  lcl|FitnessBrowser__Keio:16881  81 DSIPSFIQDVNTHGRLMLAnGQHEVEFPVDQCMNFHADNLSLHENGMRITALAGD-KVVYSQTYYSIGGGFIVDEEHFG 158
                                     ******************9789********************************9.9********************** PP

                       TIGR00720 158 keeeeeeevpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeecierglkaegvlpGglkvk 236
                                     ++++  +evpyp++saa+l ++C+e+gls+s ++++ne al+s+ee +++l+++w+vm+  ierg+++egvlpG l+v+
  lcl|FitnessBrowser__Keio:16881 159 QQDSAPVEVPYPYSSAADLQKHCQETGLSLSGLMMKNELALHSKEELEQHLANVWEVMRGGIERGISTEGVLPGKLRVP 237
                                     ******************************************************************************* PP

                       TIGR00720 237 rraaslkrklkakeetskdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrfl 315
                                     rraa+l+r+l ++++t++dp+av+dw+n++alavneenaaGgrvvtaPtnGa+giiPavlayy+kf++e++ +++ r+l
  lcl|FitnessBrowser__Keio:16881 238 RRAAALRRMLVSQDKTTTDPMAVVDWINMFALAVNEENAAGGRVVTAPTNGACGIIPAVLAYYDKFIREVNANSLARYL 316
                                     ******************************************************************************* PP

                       TIGR00720 316 ltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCier 394
                                     l+a+aiG+lyk+nasisgaevGCqgevGvacsmaaaglaellg++p qv++aaeiamehnlGltCdPv+G+vq+PCier
  lcl|FitnessBrowser__Keio:16881 317 LVASAIGSLYKMNASISGAEVGCQGEVGVACSMAAAGLAELLGASPAQVCIAAEIAMEHNLGLTCDPVAGQVQVPCIER 395
                                     ******************************************************************************* PP

                       TIGR00720 395 naiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                     naiaavka+naar+al+++++++v ldkvietm+etGkdm+aky+ets+gGla+k+
  lcl|FitnessBrowser__Keio:16881 396 NAIAAVKAVNAARMALRRTSEPRVCLDKVIETMYETGKDMNAKYRETSRGGLAMKI 451
                                     *****************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (455 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: 10.43
//
[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