Alignments for a candidate for sdaB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Burkholderia phytofirmans PsJN

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate BPHYT_RS25100 BPHYT_RS25100 serine dehydratase

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



>FitnessBrowser__BFirm:BPHYT_RS25100
          Length = 464

 Score =  632 bits (1630), Expect = 0.0
 Identities = 326/473 (68%), Positives = 372/473 (78%), Gaps = 16/473 (3%)

Query: 1   MSVSVFDLFKIGIGPSSSHTVGPMIAARQFACHVQGTLGLDAVHHVTVELFGSLSATGVG 60
           M+VSVFDLFKIGIGPSSSHTVGPMIAA +FA H++    L  V  V V+LFGSL ATG G
Sbjct: 1   MNVSVFDLFKIGIGPSSSHTVGPMIAACRFASHIEDANLLGFVRGVKVDLFGSLGATGKG 60

Query: 61  HGTDKAVLLGLAGHEPDHIDPDQILPAIADIRTRQTLALLGEHPVPFVEKEHLLFRRKSL 120
           HGTDKAVLLGL G+ PD IDPD I P +  IR  + L LLG+HPV F E+EHL F RK +
Sbjct: 61  HGTDKAVLLGLEGNLPDSIDPDLIEPRLQAIRVTKQLVLLGKHPVKFDEREHLGFFRKLM 120

Query: 121 P-------LHPNGMAFHAFDAQGNEIATREYYSVGGGFVIDAAGERVLNSAATAGPDAVG 173
           P       +HPNGM F AFD  G  +  +EYYSVGGGFV++  G+RV  +   AG +   
Sbjct: 121 PGAPGSGIVHPNGMRFQAFDENGQLLVEKEYYSVGGGFVVNREGDRV--NGVRAGAE--- 175

Query: 174 HAQGLPHPFRTGAELLAQCQATGLTPAQLMAANEQHWRSASEVRRQLMAIWKTMAGAVQR 233
               +P+PFRTG +L+  C+ TGL+ AQ+   NE   R   EVR  L+AIW+TM+  V+R
Sbjct: 176 ----VPYPFRTGDDLMRVCRETGLSIAQITLRNECAARPEQEVREGLLAIWRTMSACVER 231

Query: 234 GCASTGTLPGPMHVRRRAAELHHKLSSAPEAALRDPLSMLDWVNLYAMAVNEENAAGGRV 293
           GC   G LPGPMHV+RRAA+L  +L S  E +LRDPLSMLDWVNLYAMAVNEENAAGGRV
Sbjct: 232 GCKVRGELPGPMHVKRRAADLCGQLRSRSEESLRDPLSMLDWVNLYAMAVNEENAAGGRV 291

Query: 294 VTAPTNGAAGVIPAVLHYYVNFLPGANEDGIATFLLTAGAIGIIYKENASLSGAEVGCQG 353
           VTAPTNGAAGVIPAVLHYYV F+  +N++GI  FLLTA AIGIIYKE AS+SGAEVGCQG
Sbjct: 292 VTAPTNGAAGVIPAVLHYYVKFMHASNDEGIVNFLLTAAAIGIIYKETASISGAEVGCQG 351

Query: 354 EVGVACSMAAGALAAVMGGSPEQIENAAEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAI 413
           EVGVACSMAA ALAAVMGG+P Q+ENAAEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAI
Sbjct: 352 EVGVACSMAAAALAAVMGGTPTQVENAAEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAI 411

Query: 414 KAINAARMALRGDGQHVVSLDKVIKTMMQTGADMKVKYKETSRGGLAVNVVEC 466
           KA+NAARMA++GDGQH VSLD VIKTM +TGADMK KYKETSRGGLAVNV+EC
Sbjct: 412 KALNAARMAMKGDGQHYVSLDNVIKTMRETGADMKTKYKETSRGGLAVNVIEC 464


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: 714
Number of extensions: 25
Number of successful extensions: 3
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: 464
Length adjustment: 33
Effective length of query: 433
Effective length of database: 431
Effective search space:   186623
Effective search space used:   186623
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 BPHYT_RS25100 BPHYT_RS25100 (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.30955.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.8e-222  724.4   0.1   3.1e-222  724.2   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS25100  BPHYT_RS25100 serine dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS25100  BPHYT_RS25100 serine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  724.2   0.1  3.1e-222  3.1e-222       1     450 []       3     461 ..       3     461 .. 0.99

  Alignments for each domain:
  == domain 1  score: 724.2 bits;  conditional E-value: 3.1e-222
                                TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGle 70 
                                              +svfdlfkiGiGPssshtvGPm aa++f++++++++ l  v+ vkvdl+Gsl++tGkGh+tdkavllGle
  lcl|FitnessBrowser__BFirm:BPHYT_RS25100   3 VSVFDLFKIGIGPSSSHTVGPMIAACRFASHIEDANLLGFVRGVKVDLFGSLGATGKGHGTDKAVLLGLE 72 
                                              69******************************************************************** PP

                                TIGR00720  71 Gelpeevdiesieklleeveeekklklanqkeikfdlekdlafkdevlp.......lhenglrlkaydee 133
                                              G+lp+++d + ie +l++++ +k+l l++++ +kfd++++l f ++ +p       +h+ng+r++a+de+
  lcl|FitnessBrowser__BFirm:BPHYT_RS25100  73 GNLPDSIDPDLIEPRLQAIRVTKQLVLLGKHPVKFDEREHLGFFRKLMPgapgsgiVHPNGMRFQAFDEN 142
                                              *************************************************99999999************* PP

                                TIGR00720 134 gevlkektyysvGGGfivdeeelkkeeeeee.evpypfksaaellelCkeeglsisevvlenekalrsee 202
                                              g++l+ek+yysvGGGf+v++e  + +  ++  evpypf++ ++l++ C+e+glsi+++ l+ne+a+r+e+
  lcl|FitnessBrowser__BFirm:BPHYT_RS25100 143 GQLLVEKEYYSVGGGFVVNREGDRVNGVRAGaEVPYPFRTGDDLMRVCRETGLSIAQITLRNECAARPEQ 212
                                              *********************99999888777************************************** PP

                                TIGR00720 203 evraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeets.kdplavldwvnlyalavn 271
                                              evr+ ll+iw++m++c+erg+k  g lpG+++vkrraa l  +l++++e+s +dpl++ldwvnlya+avn
  lcl|FitnessBrowser__BFirm:BPHYT_RS25100 213 EVREGLLAIWRTMSACVERGCKVRGELPGPMHVKRRAADLCGQLRSRSEESlRDPLSMLDWVNLYAMAVN 282
                                              **********************************************999999****************** PP

                                TIGR00720 272 eenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqge 341
                                              eenaaGgrvvtaPtnGaag+iPavl+yy kf++ +++e +v+fllta+aiGi+yke+asisgaevGCqge
  lcl|FitnessBrowser__BFirm:BPHYT_RS25100 283 EENAAGGRVVTAPTNGAAGVIPAVLHYYVKFMHASNDEGIVNFLLTAAAIGIIYKETASISGAEVGCQGE 352
                                              ********************************************************************** PP

                                TIGR00720 342 vGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalk 411
                                              vGvacsmaaa+la+++ggtp+qvenaaei+mehnlG+tCdPvgGlvqiPCierna++a+ka+naar+a+k
  lcl|FitnessBrowser__BFirm:BPHYT_RS25100 353 VGVACSMAAAALAAVMGGTPTQVENAAEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAIKALNAARMAMK 422
                                              ********************************************************************** PP

                                TIGR00720 412 edgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                              +dg+++vsld+vi+tmretG+dmk+kykets+gGlav+v
  lcl|FitnessBrowser__BFirm:BPHYT_RS25100 423 GDGQHYVSLDNVIKTMRETGADMKTKYKETSRGGLAVNV 461
                                              *************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (464 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: 00:00:00.03
# Mc/sec: 6.77
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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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