Alignments for a candidate for sdaB in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Paraburkholderia bryophila 376MFSha3.1

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate H281DRAFT_02455 H281DRAFT_02455 L-serine ammonia-lyase

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



>FitnessBrowser__Burk376:H281DRAFT_02455
          Length = 464

 Score =  632 bits (1630), Expect = 0.0
 Identities = 326/473 (68%), Positives = 373/473 (78%), Gaps = 16/473 (3%)

Query: 1   MSVSVFDLFKIGIGPSSSHTVGPMIAARQFACHVQGTLGLDAVHHVTVELFGSLSATGVG 60
           M+VSVFDLFKIGIGPSSSHTVGPMIAA +FA H++    L  V  V VELFGSL ATG G
Sbjct: 1   MNVSVFDLFKIGIGPSSSHTVGPMIAACRFASHIEDANLLGFVRRVKVELFGSLGATGKG 60

Query: 61  HGTDKAVLLGLAGHEPDHIDPDQILPAIADIRTRQTLALLGEHPVPFVEKEHLLFRRKSL 120
           HGTDKAVLLGL G+ P+ IDPD I P +  IR  + LALLG+HPV F E+EHL F RK +
Sbjct: 61  HGTDKAVLLGLEGNLPELIDPDTIEPRLLAIRETKQLALLGKHPVKFDEREHLGFFRKLM 120

Query: 121 P-------LHPNGMAFHAFDAQGNEIATREYYSVGGGFVIDAAGERVLNSAATAGPDAVG 173
           P       +HPNGM F AFD  G  +  +EYYS+GGGFV++  G+RV  +   AG +   
Sbjct: 121 PGAPGSGIVHPNGMRFQAFDEYGQLLVEKEYYSIGGGFVVNREGDRV--NGVRAGAE--- 175

Query: 174 HAQGLPHPFRTGAELLAQCQATGLTPAQLMAANEQHWRSASEVRRQLMAIWKTMAGAVQR 233
               +P+PFRTG +L+  C+ TGL+ AQ+   NE   RS  EVR  L+AIW+ M+  V+R
Sbjct: 176 ----VPYPFRTGDDLMRVCRETGLSIAQVTLRNECASRSEQEVREGLLAIWRAMSACVER 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: 700
Number of extensions: 24
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 H281DRAFT_02455 H281DRAFT_02455 (L-serine ammonia-lyase)
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.19666.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.5e-222  723.4   0.1   6.3e-222  723.2   0.1    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_02455  H281DRAFT_02455 L-serine ammonia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_02455  H281DRAFT_02455 L-serine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  723.2   0.1  6.3e-222  6.3e-222       1     450 []       3     461 ..       3     461 .. 0.99

  Alignments for each domain:
  == domain 1  score: 723.2 bits;  conditional E-value: 6.3e-222
                                    TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavl 66 
                                                  +svfdlfkiGiGPssshtvGPm aa++f++++++++ l  v+rvkv+l+Gsl++tGkGh+tdkavl
  lcl|FitnessBrowser__Burk376:H281DRAFT_02455   3 VSVFDLFKIGIGPSSSHTVGPMIAACRFASHIEDANLLGFVRRVKVELFGSLGATGKGHGTDKAVL 68 
                                                  69**************************************************************** PP

                                    TIGR00720  67 lGleGelpeevdiesieklleeveeekklklanqkeikfdlekdlafkdevlp.......lhengl 125
                                                  lGleG+lpe +d ++ie +l +++e+k+l+l++++ +kfd++++l f ++ +p       +h+ng+
  lcl|FitnessBrowser__Burk376:H281DRAFT_02455  69 LGLEGNLPELIDPDTIEPRLLAIRETKQLALLGKHPVKFDEREHLGFFRKLMPgapgsgiVHPNGM 134
                                                  *****************************************************99999999***** PP

                                    TIGR00720 126 rlkaydeegevlkektyysvGGGfivdeeelkkeeeeee.evpypfksaaellelCkeeglsisev 190
                                                  r++a+de g++l+ek+yys+GGGf+v++e  + +  ++  evpypf++ ++l++ C+e+glsi++v
  lcl|FitnessBrowser__Burk376:H281DRAFT_02455 135 RFQAFDEYGQLLVEKEYYSIGGGFVVNREGDRVNGVRAGaEVPYPFRTGDDLMRVCRETGLSIAQV 200
                                                  *****************************99999888777************************** PP

                                    TIGR00720 191 vlenekalrseeevraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeets.kd 255
                                                   l+ne+a rse+evr+ ll+iw++m++c+erg+k  g lpG+++vkrraa l  +l++++e+s +d
  lcl|FitnessBrowser__Burk376:H281DRAFT_02455 201 TLRNECASRSEQEVREGLLAIWRAMSACVERGCKVRGELPGPMHVKRRAADLCGQLRSRSEESlRD 266
                                                  **********************************************************999999** PP

                                    TIGR00720 256 plavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagai 321
                                                  pl++ldwvnlya+avneenaaGgrvvtaPtnGaag+iPavl+yy kf++ +++e +v+fllta+ai
  lcl|FitnessBrowser__Burk376:H281DRAFT_02455 267 PLSMLDWVNLYAMAVNEENAAGGRVVTAPTNGAAGVIPAVLHYYVKFMHASNDEGIVNFLLTAAAI 332
                                                  ****************************************************************** PP

                                    TIGR00720 322 GilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlv 387
                                                  Gi+yke+asisgaevGCqgevGvacsmaaa+la+++ggtp+qvenaaei+mehnlG+tCdPvgGlv
  lcl|FitnessBrowser__Burk376:H281DRAFT_02455 333 GIIYKETASISGAEVGCQGEVGVACSMAAAALAAVMGGTPTQVENAAEIGMEHNLGMTCDPVGGLV 398
                                                  ****************************************************************** PP

                                    TIGR00720 388 qiPCiernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                                  qiPCierna++a+ka+naar+a+k+dg+++vsld+vi+tmretG+dmk+kykets+gGlav+v
  lcl|FitnessBrowser__Burk376:H281DRAFT_02455 399 QIPCIERNAMGAIKALNAARMAMKGDGQHYVSLDNVIKTMRETGADMKTKYKETSRGGLAVNV 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: 00:00:00.02
# Mc/sec: 7.88
//
[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