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

GapMind for catabolism of small carbon sources

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

Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate H281DRAFT_01568 H281DRAFT_01568 D-serine ammonia-lyase

Query= BRENDA::Q9HYN9
         (448 letters)



>FitnessBrowser__Burk376:H281DRAFT_01568
          Length = 453

 Score =  629 bits (1622), Expect = 0.0
 Identities = 309/446 (69%), Positives = 355/446 (79%)

Query: 2   ILGTPKADWLAEFPRLADLIALRPSEWFNPAIAPSAEALADVGLGAADVADASARLQRFA 61
           I G P   WL ++P L  L+ L+P EWFNPA+AP  +A+ D+ L A+DVADASARLQRFA
Sbjct: 5   IYGKPLDAWLRDYPLLRPLMELQPVEWFNPAVAPLVDAIDDIPLDASDVADASARLQRFA 64

Query: 62  PLIARLFPETAASGGIIESDLVEVATFHDALRQHYAAELPGRLWLKRDSHLPISGSIKAR 121
           PL+A+ F +   +GGIIES L EV  F DAL + Y  E P RL LK+DSHLP+SGSIKAR
Sbjct: 65  PLLAQTFDDVREAGGIIESPLTEVPLFADALSRRYEVETPRRLLLKQDSHLPVSGSIKAR 124

Query: 122 GGIYEVLAHAERLALEHGLVGLDDDYSRLAEADCRAFFARHRIAVGSTGNLGLSIGIIGA 181
           GGIYEVL HAE+LA+ HGL+   DDY  LA   CRA F +H IAVGSTGNLG+SIGI  A
Sbjct: 125 GGIYEVLFHAEQLAIRHGLLNEGDDYRVLATDACRALFRKHSIAVGSTGNLGMSIGIASA 184

Query: 182 ALGFQASVHMSADARQWKKDKLRAHGVTVVEYASDYSVAVEQGRREAAGDPYTHFVDDEN 241
            LGF  +VHMSADARQWKKD+LRAHGVTV+EYA DY  A+E GRR A+ DP  HFVDDEN
Sbjct: 185 TLGFTTTVHMSADARQWKKDRLRAHGVTVIEYAGDYGEAIESGRRLASNDPLCHFVDDEN 244

Query: 242 SRDLFLGYAVAAERLRGQLDAAGIRVDSEHPLFVHLPCGVGGGPGGVAFGLKLAFGDAVH 301
           S  LFLGYAVA ERL+ Q DAA + VD  HPLFV+LPCGVGGGPGGVAFGLKLAFGDAVH
Sbjct: 245 STTLFLGYAVAGERLKRQFDAANVPVDGGHPLFVYLPCGVGGGPGGVAFGLKLAFGDAVH 304

Query: 302 CLFAEPTHSPCMFLGVYTGRHEQVSVQDFGIDNRTAADGLAVGRPSGFVGRAMQRLLDGY 361
           C+FAEPTHSPCM +GV TG HE+++VQDFGIDN TAADGLAVGRPSGFVGRAMQR++DGY
Sbjct: 305 CVFAEPTHSPCMLMGVLTGLHEKLAVQDFGIDNLTAADGLAVGRPSGFVGRAMQRMIDGY 364

Query: 362 YTVDDDELFRLLALLERSQGIRLEPSALAGATGIARVTREPQGYRERMGLTSARLANATH 421
           YT+DD EL+ LLAL+  +Q IRLEPSALAGA G ARV +E QGYR RM L  A + NATH
Sbjct: 365 YTIDDRELYALLALMADTQAIRLEPSALAGAPGFARVLKEAQGYRARMALDDAAMRNATH 424

Query: 422 LVWATGGGMVPETEMRAYLERGRSLL 447
           ++WATGGGMVPE EM AYL+ GR+ L
Sbjct: 425 VIWATGGGMVPEVEMSAYLQTGRAAL 450


Lambda     K      H
   0.321    0.138    0.414 

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: 626
Number of extensions: 18
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: 448
Length of database: 453
Length adjustment: 33
Effective length of query: 415
Effective length of database: 420
Effective search space:   174300
Effective search space used:   174300
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 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate H281DRAFT_01568 H281DRAFT_01568 (D-serine ammonia-lyase)
to HMM TIGR02035 (dsdA: D-serine ammonia-lyase (EC 4.3.1.18))

# 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/TIGR02035.hmm
# target sequence database:        /tmp/gapView.24101.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02035  [M=431]
Accession:   TIGR02035
Description: D_Ser_am_lyase: D-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.8e-211  686.7   0.0   6.6e-211  686.5   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01568  H281DRAFT_01568 D-serine ammonia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01568  H281DRAFT_01568 D-serine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  686.5   0.0  6.6e-211  6.6e-211       1     431 []      13     443 ..      13     443 .. 1.00

  Alignments for each domain:
  == domain 1  score: 686.5 bits;  conditional E-value: 6.6e-211
                                    TIGR02035   1 lllkeplikdlidlkevewanpkkaslaealkkvdlkeqevkeaearlkrfapyiakvfpetaatk 66 
                                                  +l ++pl++ l++l++vew+np+ a+l +a+ +++l +++v++a+arl+rfap++a+ f + ++++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01568  13 WLRDYPLLRPLMELQPVEWFNPAVAPLVDAIDDIPLDASDVADASARLQRFAPLLAQTFDDVREAG 78 
                                                  57789************************************************************* PP

                                    TIGR02035  67 GiieselvevaalkkklekkyqqelsGrlllkkdshlpisGsikarGGiyevlkhaeklaleaGll 132
                                                  Giies+l+ev  + ++l ++y+ e + rlllk+dshlp+sGsikarGGiyevl hae+la+++Gll
  lcl|FitnessBrowser__Burk376:H281DRAFT_01568  79 GIIESPLTEVPLFADALSRRYEVETPRRLLLKQDSHLPVSGSIKARGGIYEVLFHAEQLAIRHGLL 144
                                                  ****************************************************************** PP

                                    TIGR02035 133 kldddysklaeeefkdffsrykiavGstGnlGlsiGiisaalGfkvtvhmsadakkwkkdklrskG 198
                                                  ++ ddy+ la + ++++f +++iavGstGnlG+siGi sa+lGf  tvhmsada++wkkd+lr++G
  lcl|FitnessBrowser__Burk376:H281DRAFT_01568 145 NEGDDYRVLATDACRALFRKHSIAVGSTGNLGMSIGIASATLGFTTTVHMSADARQWKKDRLRAHG 210
                                                  ****************************************************************** PP

                                    TIGR02035 199 vtvveyesdyskaveeGrkeaeadplsyfvddeksrdlflGyavaasrlkkqldkkgikvdkehpl 264
                                                  vtv+ey+ dy++a+e Gr+ a++dpl++fvdde+s +lflGyava++rlk q+d++++ vd  hpl
  lcl|FitnessBrowser__Burk376:H281DRAFT_01568 211 VTVIEYAGDYGEAIESGRRLASNDPLCHFVDDENSTTLFLGYAVAGERLKRQFDAANVPVDGGHPL 276
                                                  ****************************************************************** PP

                                    TIGR02035 265 fvylpcGvGGgpGGvafGlkllfgddvhvffaepthspcmllGlytGlhekisvqdiGidnltaad 330
                                                  fvylpcGvGGgpGGvafGlkl+fgd+vh++faepthspcml+G+ tGlhek++vqd+Gidnltaad
  lcl|FitnessBrowser__Burk376:H281DRAFT_01568 277 FVYLPCGVGGGPGGVAFGLKLAFGDAVHCVFAEPTHSPCMLMGVLTGLHEKLAVQDFGIDNLTAAD 342
                                                  ****************************************************************** PP

                                    TIGR02035 331 GlavgrpsGlvGrllerlldGiytvddeklydllallaesedkrlepsalaglaGvvrllkeeesk 396
                                                  GlavgrpsG+vGr+++r++dG+yt+dd++ly llal+a ++ +rlepsalag+ G +r+lke +++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01568 343 GLAVGRPSGFVGRAMQRMIDGYYTIDDRELYALLALMADTQAIRLEPSALAGAPGFARVLKEAQGY 408
                                                  ****************************************************************** PP

                                    TIGR02035 397 reaekliakklenavhlvwatGGkmvpeeemeayl 431
                                                  r ++ l  + ++na+h++watGG+mvpe em+ayl
  lcl|FitnessBrowser__Burk376:H281DRAFT_01568 409 RARMALDDAAMRNATHVIWATGGGMVPEVEMSAYL 443
                                                  *********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (431 nodes)
Target sequences:                          1  (453 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: 12.46
//
[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