Alignments for a candidate for sdaB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Cupriavidus basilensis 4G11

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate RR42_RS20080 RR42_RS20080 serine dehydratase

Query= reanno::Cup4G11:RR42_RS20080
         (458 letters)



>FitnessBrowser__Cup4G11:RR42_RS20080
          Length = 458

 Score =  910 bits (2351), Expect = 0.0
 Identities = 458/458 (100%), Positives = 458/458 (100%)

Query: 1   MAVSVFDLFKVGIGPSSSHTVGPMRAALMFAQGLARDGLLPQVASVRVELYGSLGATGRG 60
           MAVSVFDLFKVGIGPSSSHTVGPMRAALMFAQGLARDGLLPQVASVRVELYGSLGATGRG
Sbjct: 1   MAVSVFDLFKVGIGPSSSHTVGPMRAALMFAQGLARDGLLPQVASVRVELYGSLGATGRG 60

Query: 61  HGTDKGVILGLLGEAPDTIDPDTIDVRLAALRASRTLSLLGTHPVPFVEKEHIVFYRREA 120
           HGTDKGVILGLLGEAPDTIDPDTIDVRLAALRASRTLSLLGTHPVPFVEKEHIVFYRREA
Sbjct: 61  HGTDKGVILGLLGEAPDTIDPDTIDVRLAALRASRTLSLLGTHPVPFVEKEHIVFYRREA 120

Query: 121 MAEHPNGMKFHAFNAGGERIREGRYLSVGGGFIITAGAANTHILEADQQLPHPFRSGRAM 180
           MAEHPNGMKFHAFNAGGERIREGRYLSVGGGFIITAGAANTHILEADQQLPHPFRSGRAM
Sbjct: 121 MAEHPNGMKFHAFNAGGERIREGRYLSVGGGFIITAGAANTHILEADQQLPHPFRSGRAM 180

Query: 181 LEMAAASKKSIARLMMENECVWRSEAEVNAGLLQIWAVMQACVARGCRTDGELPGPFKVK 240
           LEMAAASKKSIARLMMENECVWRSEAEVNAGLLQIWAVMQACVARGCRTDGELPGPFKVK
Sbjct: 181 LEMAAASKKSIARLMMENECVWRSEAEVNAGLLQIWAVMQACVARGCRTDGELPGPFKVK 240

Query: 241 RRAHDLFRNLTEHAERALADPLSVIDWVNLYAIAVNEENAAGGRVVTAPTNGAAGIIPAV 300
           RRAHDLFRNLTEHAERALADPLSVIDWVNLYAIAVNEENAAGGRVVTAPTNGAAGIIPAV
Sbjct: 241 RRAHDLFRNLTEHAERALADPLSVIDWVNLYAIAVNEENAAGGRVVTAPTNGAAGIIPAV 300

Query: 301 LHYYDRFVPGANPQGVIDFLLTAGAIGMLYKLNASISGAEVGCQGEVGVACSMAAGALAA 360
           LHYYDRFVPGANPQGVIDFLLTAGAIGMLYKLNASISGAEVGCQGEVGVACSMAAGALAA
Sbjct: 301 LHYYDRFVPGANPQGVIDFLLTAGAIGMLYKLNASISGAEVGCQGEVGVACSMAAGALAA 360

Query: 361 VMGGTPEQVENAAEIGMEHNLGLTCDPVGGLVQIPCIERNAMASVKAVNAARMALRGDGM 420
           VMGGTPEQVENAAEIGMEHNLGLTCDPVGGLVQIPCIERNAMASVKAVNAARMALRGDGM
Sbjct: 361 VMGGTPEQVENAAEIGMEHNLGLTCDPVGGLVQIPCIERNAMASVKAVNAARMALRGDGM 420

Query: 421 HYVSLDSVIKTMRETGADMKTKYKETARGGLAVNIVEC 458
           HYVSLDSVIKTMRETGADMKTKYKETARGGLAVNIVEC
Sbjct: 421 HYVSLDSVIKTMRETGADMKTKYKETARGGLAVNIVEC 458


Lambda     K      H
   0.320    0.136    0.400 

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: 878
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: 458
Length of database: 458
Length adjustment: 33
Effective length of query: 425
Effective length of database: 425
Effective search space:   180625
Effective search space used:   180625
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 RR42_RS20080 RR42_RS20080 (serine dehydratase)
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.24286.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     9e-214  696.4   0.2     1e-213  696.2   0.2    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS20080  RR42_RS20080 serine dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS20080  RR42_RS20080 serine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  696.2   0.2    1e-213    1e-213       1     450 []       3     455 ..       3     455 .. 0.98

  Alignments for each domain:
  == domain 1  score: 696.2 bits;  conditional E-value: 1e-213
                                 TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGl 69 
                                               +svfdlfk+GiGPssshtvGPm+aa +f++ l + g l qv++v+v+lyGsl++tG+Gh+tdk v+lGl
  lcl|FitnessBrowser__Cup4G11:RR42_RS20080   3 VSVFDLFKVGIGPSSSHTVGPMRAALMFAQGLARDGLLPQVASVRVELYGSLGATGRGHGTDKGVILGL 71 
                                               69******************************************************************* PP

                                 TIGR00720  70 eGelpeevdiesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegevl 137
                                                Ge p+++d ++i+ +l++++++++l+l++++ + f ++++++f+ +e++ +h+ng++++a++  ge +
  lcl|FitnessBrowser__Cup4G11:RR42_RS20080  72 LGEAPDTIDPDTIDVRLAALRASRTLSLLGTHPVPFVEKEHIVFYrREAMAEHPNGMKFHAFNAGGERI 140
                                               ********************************************9899********************* PP

                                 TIGR00720 138 kektyysvGGGfivdeeelkkee.eeeeevpypfksaaellelCkeeglsisevvlenekalrseeevr 205
                                               +e  y svGGGfi++  +++++  e ++++p+pf+s + +le+ +++++si+++++ene+++rse+ev+
  lcl|FitnessBrowser__Cup4G11:RR42_RS20080 141 REGRYLSVGGGFIITAGAANTHIlEADQQLPHPFRSGRAMLEMAAASKKSIARLMMENECVWRSEAEVN 209
                                               ***************9888777615556***************************************** PP

                                 TIGR00720 206 aklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeets.kdplavldwvnlyalavnee 273
                                               a ll+iw vm++c+ rg++++g lpG++kvkrra+ l r+l+++ e   +dpl+v+dwvnlya+avnee
  lcl|FitnessBrowser__Cup4G11:RR42_RS20080 210 AGLLQIWAVMQACVARGCRTDGELPGPFKVKRRAHDLFRNLTEHAERAlADPLSVIDWVNLYAIAVNEE 278
                                               *******************************************999988******************** PP

                                 TIGR00720 274 naaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgev 342
                                               naaGgrvvtaPtnGaagiiPavl+yy++fv+ a+ + v++flltagaiG+lyk nasisgaevGCqgev
  lcl|FitnessBrowser__Cup4G11:RR42_RS20080 279 NAAGGRVVTAPTNGAAGIIPAVLHYYDRFVPGANPQGVIDFLLTAGAIGMLYKLNASISGAEVGCQGEV 347
                                               ********************************************************************* PP

                                 TIGR00720 343 GvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalk 411
                                               Gvacsmaa++la+++ggtpeqvenaaei+mehnlGltCdPvgGlvqiPCierna+a+vka+naar+al+
  lcl|FitnessBrowser__Cup4G11:RR42_RS20080 348 GVACSMAAGALAAVMGGTPEQVENAAEIGMEHNLGLTCDPVGGLVQIPCIERNAMASVKAVNAARMALR 416
                                               ********************************************************************* PP

                                 TIGR00720 412 edgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                               +dg ++vsld+vi+tmretG+dmk+kyket++gGlav++
  lcl|FitnessBrowser__Cup4G11:RR42_RS20080 417 GDGMHYVSLDSVIKTMRETGADMKTKYKETARGGLAVNI 455
                                               *************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (458 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: 12.25
//
[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