Alignments for a candidate for sdaB in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Acidovorax sp. GW101-3H11

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate Ac3H11_929 L-serine dehydratase (EC 4.3.1.17)

Query= reanno::acidovorax_3H11:Ac3H11_929
         (466 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_929
          Length = 466

 Score =  931 bits (2407), Expect = 0.0
 Identities = 466/466 (100%), Positives = 466/466 (100%)

Query: 1   MSVSVFDLFKIGIGPSSSHTVGPMIAARQFACHVQGTLGLDAVHHVTVELFGSLSATGVG 60
           MSVSVFDLFKIGIGPSSSHTVGPMIAARQFACHVQGTLGLDAVHHVTVELFGSLSATGVG
Sbjct: 1   MSVSVFDLFKIGIGPSSSHTVGPMIAARQFACHVQGTLGLDAVHHVTVELFGSLSATGVG 60

Query: 61  HGTDKAVLLGLAGHEPDHIDPDQILPAIADIRTRQTLALLGEHPVPFVEKEHLLFRRKSL 120
           HGTDKAVLLGLAGHEPDHIDPDQILPAIADIRTRQTLALLGEHPVPFVEKEHLLFRRKSL
Sbjct: 61  HGTDKAVLLGLAGHEPDHIDPDQILPAIADIRTRQTLALLGEHPVPFVEKEHLLFRRKSL 120

Query: 121 PLHPNGMAFHAFDAQGNEIATREYYSVGGGFVIDAAGERVLNSAATAGPDAVGHAQGLPH 180
           PLHPNGMAFHAFDAQGNEIATREYYSVGGGFVIDAAGERVLNSAATAGPDAVGHAQGLPH
Sbjct: 121 PLHPNGMAFHAFDAQGNEIATREYYSVGGGFVIDAAGERVLNSAATAGPDAVGHAQGLPH 180

Query: 181 PFRTGAELLAQCQATGLTPAQLMAANEQHWRSASEVRRQLMAIWKTMAGAVQRGCASTGT 240
           PFRTGAELLAQCQATGLTPAQLMAANEQHWRSASEVRRQLMAIWKTMAGAVQRGCASTGT
Sbjct: 181 PFRTGAELLAQCQATGLTPAQLMAANEQHWRSASEVRRQLMAIWKTMAGAVQRGCASTGT 240

Query: 241 LPGPMHVRRRAAELHHKLSSAPEAALRDPLSMLDWVNLYAMAVNEENAAGGRVVTAPTNG 300
           LPGPMHVRRRAAELHHKLSSAPEAALRDPLSMLDWVNLYAMAVNEENAAGGRVVTAPTNG
Sbjct: 241 LPGPMHVRRRAAELHHKLSSAPEAALRDPLSMLDWVNLYAMAVNEENAAGGRVVTAPTNG 300

Query: 301 AAGVIPAVLHYYVNFLPGANEDGIATFLLTAGAIGIIYKENASLSGAEVGCQGEVGVACS 360
           AAGVIPAVLHYYVNFLPGANEDGIATFLLTAGAIGIIYKENASLSGAEVGCQGEVGVACS
Sbjct: 301 AAGVIPAVLHYYVNFLPGANEDGIATFLLTAGAIGIIYKENASLSGAEVGCQGEVGVACS 360

Query: 361 MAAGALAAVMGGSPEQIENAAEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAIKAINAAR 420
           MAAGALAAVMGGSPEQIENAAEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAIKAINAAR
Sbjct: 361 MAAGALAAVMGGSPEQIENAAEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAIKAINAAR 420

Query: 421 MALRGDGQHVVSLDKVIKTMMQTGADMKVKYKETSRGGLAVNVVEC 466
           MALRGDGQHVVSLDKVIKTMMQTGADMKVKYKETSRGGLAVNVVEC
Sbjct: 421 MALRGDGQHVVSLDKVIKTMMQTGADMKVKYKETSRGGLAVNVVEC 466


Lambda     K      H
   0.319    0.134    0.398 

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: 979
Number of extensions: 32
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: 466
Length of database: 466
Length adjustment: 33
Effective length of query: 433
Effective length of database: 433
Effective search space:   187489
Effective search space used:   187489
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 Ac3H11_929 (L-serine dehydratase (EC 4.3.1.17))
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.4325.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
     1e-211  689.6   0.9   1.2e-211  689.4   0.9    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_929  L-serine dehydratase (EC 4.3.1.1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_929  L-serine dehydratase (EC 4.3.1.17)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  689.4   0.9  1.2e-211  1.2e-211       1     450 []       3     463 ..       3     463 .. 0.97

  Alignments for each domain:
  == domain 1  score: 689.4 bits;  conditional E-value: 1.2e-211
                                       TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdk 63 
                                                     +svfdlfkiGiGPssshtvGPm aa++f+ +++    l++v++v+v+l+Gsl++tG Gh+tdk
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_929   3 VSVFDLFKIGIGPSSSHTVGPMIAARQFACHVQGTLGLDAVHHVTVELFGSLSATGVGHGTDK 65 
                                                     69************************************************************* PP

                                       TIGR00720  64 avllGleGelpeevdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglr 126
                                                     avllGl+G++p+++d ++i   +++++++++l+l++++ + f ++++l f++++lplh+ng+ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_929  66 AVLLGLAGHEPDHIDPDQILPAIADIRTRQTLALLGEHPVPFVEKEHLLFRRKSLPLHPNGMA 128
                                                     *************************************************************** PP

                                       TIGR00720 127 lkaydeegevlkektyysvGGGfivdeeelkkeeeeee..........evpypfksaaellel 179
                                                     ++a+d +g+ +++++yysvGGGf++d +  +  ++ ++           +p+pf++ aell++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_929 129 FHAFDAQGNEIATREYYSVGGGFVIDAAGERVLNSAATagpdavghaqGLPHPFRTGAELLAQ 191
                                                     *************************9877665544433345556666679************* PP

                                       TIGR00720 180 CkeeglsisevvlenekalrseeevraklleiwkvmeecierglkaegvlpGglkvkrraasl 242
                                                     C+++gl+ ++++ +ne+ +rs +evr++l++iwk+m+ +++rg+++ g+lpG+++v+rraa+l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_929 192 CQATGLTPAQLMAANEQHWRSASEVRRQLMAIWKTMAGAVQRGCASTGTLPGPMHVRRRAAEL 254
                                                     *************************************************************** PP

                                       TIGR00720 243 krklkakeets.kdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfve 304
                                                     ++kl++  e+  +dpl++ldwvnlya+avneenaaGgrvvtaPtnGaag+iPavl+yy +f +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_929 255 HHKLSSAPEAAlRDPLSMLDWVNLYAMAVNEENAAGGRVVTAPTNGAAGVIPAVLHYYVNFLP 317
                                                     *******99999*************************************************** PP

                                       TIGR00720 305 easeekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvena 367
                                                      a+e+ +  flltagaiGi+ykenas+sgaevGCqgevGvacsmaa++la+++gg+peq+ena
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_929 318 GANEDGIATFLLTAGAIGIIYKENASLSGAEVGCQGEVGVACSMAAGALAAVMGGSPEQIENA 380
                                                     *************************************************************** PP

                                       TIGR00720 368 aeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgkkkvsldkvietmret 430
                                                     aei+mehnlG+tCdPvgGlvqiPCierna++a+kainaar+al++dg++ vsldkvi+tm++t
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_929 381 AEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAIKAINAARMALRGDGQHVVSLDKVIKTMMQT 443
                                                     *************************************************************** PP

                                       TIGR00720 431 GkdmkakyketskgGlavkv 450
                                                     G+dmk kykets+gGlav+v
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_929 444 GADMKVKYKETSRGGLAVNV 463
                                                     ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (466 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: 00:00:00.01
# Mc/sec: 12.24
//
[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