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 1936936 b4471 L-serine dehydratase 3 (NCBI)

Query= BRENDA::P42630
         (454 letters)



>FitnessBrowser__Keio:1936936
          Length = 454

 Score =  902 bits (2331), Expect = 0.0
 Identities = 454/454 (100%), Positives = 454/454 (100%)

Query: 1   MISAFDIFKIGIGPSSSHTVGPMNAGKSFIDRLESSGLLTATSHIVVDLYGSLSLTGKGH 60
           MISAFDIFKIGIGPSSSHTVGPMNAGKSFIDRLESSGLLTATSHIVVDLYGSLSLTGKGH
Sbjct: 1   MISAFDIFKIGIGPSSSHTVGPMNAGKSFIDRLESSGLLTATSHIVVDLYGSLSLTGKGH 60

Query: 61  ATDVAIIMGLAGNSPQDVVIDEIPAFIELVTRSGRLPVASGAHIVDFPVAKNIIFHPEML 120
           ATDVAIIMGLAGNSPQDVVIDEIPAFIELVTRSGRLPVASGAHIVDFPVAKNIIFHPEML
Sbjct: 61  ATDVAIIMGLAGNSPQDVVIDEIPAFIELVTRSGRLPVASGAHIVDFPVAKNIIFHPEML 120

Query: 121 PRHENGMRITAWKGQEELLSKTYYSVGGGFIVEEEHFGLSHDVETSVPYDFHSAGELLKM 180
           PRHENGMRITAWKGQEELLSKTYYSVGGGFIVEEEHFGLSHDVETSVPYDFHSAGELLKM
Sbjct: 121 PRHENGMRITAWKGQEELLSKTYYSVGGGFIVEEEHFGLSHDVETSVPYDFHSAGELLKM 180

Query: 181 CDYNGLSISGLMMHNELALRSKAEIDAGFARIWQVMHDGIERGMNTEGVLPGPLNVPRRA 240
           CDYNGLSISGLMMHNELALRSKAEIDAGFARIWQVMHDGIERGMNTEGVLPGPLNVPRRA
Sbjct: 181 CDYNGLSISGLMMHNELALRSKAEIDAGFARIWQVMHDGIERGMNTEGVLPGPLNVPRRA 240

Query: 241 VALRRQLVSSDNISNDPMNVIDWINMYALAVSEENAAGGRVVTAPTNGACGIIPAVLAYY 300
           VALRRQLVSSDNISNDPMNVIDWINMYALAVSEENAAGGRVVTAPTNGACGIIPAVLAYY
Sbjct: 241 VALRRQLVSSDNISNDPMNVIDWINMYALAVSEENAAGGRVVTAPTNGACGIIPAVLAYY 300

Query: 301 DKFRRPVNERSIARYFLAAGAIGALYKMNASISGAEVGCQGEIGVACSMAAAGLTELLGG 360
           DKFRRPVNERSIARYFLAAGAIGALYKMNASISGAEVGCQGEIGVACSMAAAGLTELLGG
Sbjct: 301 DKFRRPVNERSIARYFLAAGAIGALYKMNASISGAEVGCQGEIGVACSMAAAGLTELLGG 360

Query: 361 SPAQVCNAAEIAMEHNLGLTCDPVAGQVQIPCIERNAINAVKAVNAARMAMRRTSAPRVS 420
           SPAQVCNAAEIAMEHNLGLTCDPVAGQVQIPCIERNAINAVKAVNAARMAMRRTSAPRVS
Sbjct: 361 SPAQVCNAAEIAMEHNLGLTCDPVAGQVQIPCIERNAINAVKAVNAARMAMRRTSAPRVS 420

Query: 421 LDKVIETMYETGKDMNDKYRETSRGGLAIKVVCG 454
           LDKVIETMYETGKDMNDKYRETSRGGLAIKVVCG
Sbjct: 421 LDKVIETMYETGKDMNDKYRETSRGGLAIKVVCG 454


Lambda     K      H
   0.319    0.135    0.395 

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: 895
Number of extensions: 19
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: 454
Length of database: 454
Length adjustment: 33
Effective length of query: 421
Effective length of database: 421
Effective search space:   177241
Effective search space used:   177241
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 1936936 b4471 (L-serine dehydratase 3 (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.1867.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.1e-222  723.3   0.1   6.9e-222  723.1   0.1    1.0  1  lcl|FitnessBrowser__Keio:1936936  b4471 L-serine dehydratase 3 (NC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:1936936  b4471 L-serine dehydratase 3 (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  723.1   0.1  6.9e-222  6.9e-222       1     450 []       2     451 ..       2     451 .. 0.99

  Alignments for each domain:
  == domain 1  score: 723.1 bits;  conditional E-value: 6.9e-222
                         TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpeev 77 
                                       is fd+fkiGiGPssshtvGPm+a+k+f+++l++ g l++++++ vdlyGsl+ltGkGh+td a+++Gl+G++p++v
  lcl|FitnessBrowser__Keio:1936936   2 ISAFDIFKIGIGPSSSHTVGPMNAGKSFIDRLESSGLLTATSHIVVDLYGSLSLTGKGHATDVAIIMGLAGNSPQDV 78 
                                       799************************************************************************** PP

                         TIGR00720  78 diesieklleeveeekklkla.nqkeikfdlekdlafkdevlplhenglrlkaydeegevlkektyysvGGGfivde 153
                                        i++i++++e v+++++l +a + + ++f ++k+++f+ e+lp+heng+r++a++++ e l +ktyysvGGGfiv+e
  lcl|FitnessBrowser__Keio:1936936  79 VIDEIPAFIELVTRSGRLPVAsGAHIVDFPVAKNIIFHPEMLPRHENGMRITAWKGQ-EELLSKTYYSVGGGFIVEE 154
                                       ********************9788999****************************99.788899************* PP

                         TIGR00720 154 eelkkeeeeeeevpypfksaaellelCkeeglsisevvlenekalrseeevraklleiwkvmeecierglkaegvlp 230
                                       e+++ +++ e++vpy+f+sa ell++C+ +glsis ++++ne alrs++e++a +++iw+vm++ ierg+++egvlp
  lcl|FitnessBrowser__Keio:1936936 155 EHFGLSHDVETSVPYDFHSAGELLKMCDYNGLSISGLMMHNELALRSKAEIDAGFARIWQVMHDGIERGMNTEGVLP 231
                                       ***************************************************************************** PP

                         TIGR00720 231 GglkvkrraaslkrklkakeetskdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeas 307
                                       G+l+v+rra +l+r+l ++++ s+dp++v+dw+n+yalav+eenaaGgrvvtaPtnGa+giiPavlayy+kf + ++
  lcl|FitnessBrowser__Keio:1936936 232 GPLNVPRRAVALRRQLVSSDNISNDPMNVIDWINMYALAVSEENAAGGRVVTAPTNGACGIIPAVLAYYDKFRRPVN 308
                                       ***************************************************************************** PP

                         TIGR00720 308 eekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvg 384
                                       e ++ r++l+agaiG+lyk+nasisgaevGCqge+Gvacsmaaagl+ellgg+p qv+naaeiamehnlGltCdPv+
  lcl|FitnessBrowser__Keio:1936936 309 ERSIARYFLAAGAIGALYKMNASISGAEVGCQGEIGVACSMAAAGLTELLGGSPAQVCNAAEIAMEHNLGLTCDPVA 385
                                       ***************************************************************************** PP

                         TIGR00720 385 GlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                       G+vqiPCiernai avka+naar+a++++++++vsldkvietm+etGkdm+ ky+ets+gGla+kv
  lcl|FitnessBrowser__Keio:1936936 386 GQVQIPCIERNAINAVKAVNAARMAMRRTSAPRVSLDKVIETMYETGKDMNDKYRETSRGGLAIKV 451
                                       ****************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (454 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.15
//
[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