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.19514.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: 00:00:00.02
# Mc/sec: 9.75
//
[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:

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:

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:

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:

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