Alignments for a candidate for dsdA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for dsdA in Acidovorax sp. GW101-3H11

Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate Ac3H11_4130 D-serine dehydratase (EC 4.3.1.18)

Query= BRENDA::Q9HYN9
         (448 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4130
          Length = 450

 Score =  399 bits (1025), Expect = e-115
 Identities = 223/443 (50%), Positives = 285/443 (64%), Gaps = 14/443 (3%)

Query: 15  PRLADLIALR-----PSEWFNPAI-APSAEALADVG--LGAADVADASARLQRFAPLIAR 66
           P +  L+A R     P+ W NPA  A  A AL  +G  +   D   A+ARL RFA L+A+
Sbjct: 8   PAIDALLATRLRNAQPALWTNPARQAQPAAALPALGRTISLDDTHAAAARLARFAGLLAQ 67

Query: 67  LFPETAASGGIIESDLVEVATFHDALRQHYAAELPGRLWLKRDSHLPISGSIKARGGIYE 126
           +FPE AA+GG++ES L+  A    AL     AE  G L++K D  LP++GSIKARGG++E
Sbjct: 68  VFPELAATGGVVESPLLPAAALAPALGM---AEAQGSLFIKADHSLPVAGSIKARGGMHE 124

Query: 127 VLAHAERLALEHGLVGLDDDYSRLAEADCRAFFARHRIAVGSTGNLGLSIGIIGAALGFQ 186
           VL  AE LAL+HGLV    DY  LA    R    R+++AVGSTGNLG+SIG++ +ALGFQ
Sbjct: 125 VLEFAEGLALQHGLVQPGGDYRALATPQAREVLGRYQVAVGSTGNLGMSIGVVASALGFQ 184

Query: 187 ASVHMSADARQWKKDKLRAHGVTVVEYASDYSVAVEQGRREAAGDPYTHFVDDENSRDLF 246
           A+VHMSADA++WKKD+LR  GV VVE+  DY  AV  GR EAA +P  HFVDDE S  L 
Sbjct: 185 ATVHMSADAKEWKKDRLRQRGVLVVEHTGDYERAVAAGRAEAASNPLCHFVDDEQSFSLL 244

Query: 247 LGYAVAAERLRGQLDAAGIRVDSEHPLFVHLPCGVGGGPGGVAFGLKLAFGDAVHCLFAE 306
           LGY+ AA  L+ QL   G+ VD+EHPL V+LPCGVGG P G+ FGL+   G  VHC FAE
Sbjct: 245 LGYSAAALHLQKQLAEQGVAVDAEHPLIVYLPCGVGGAPAGITFGLRQVLGPHVHCFFAE 304

Query: 307 PTHSPCMFLGVYTGRHEQVSVQDFGIDNRTAADGLAVGRPSGFVGRAMQRLLDGYYTVDD 366
           P  SPC  + +  G+ E  SV D+G+ NRT ADGLAV R S      MQ LL G +TV D
Sbjct: 305 PVQSPCFLVQMMAGQGEHPSVYDWGLTNRTEADGLAVPRASLLAAELMQPLLSGVFTVAD 364

Query: 367 DELFRLLALLERSQGIRLEPSALAGATGIARV--TREPQGYRERMGLTSARLANATHLVW 424
           D LF  L  +  + G R+EPSA AG +G A +  T   Q +    G+  A L  ATHLVW
Sbjct: 365 DTLFAHLVRVLDALGERIEPSAAAGFSGPALLTGTTAGQAWLRSTGI-DAVLHQATHLVW 423

Query: 425 ATGGGMVPETEMRAYLERGRSLL 447
            TGG +VP+ + + +++RGR++L
Sbjct: 424 TTGGLLVPDAQYQGFVQRGRAVL 446


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: 575
Number of extensions: 28
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: 448
Length of database: 450
Length adjustment: 33
Effective length of query: 415
Effective length of database: 417
Effective search space:   173055
Effective search space used:   173055
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 Ac3H11_4130 (D-serine dehydratase (EC 4.3.1.18))
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.9187.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.7e-152  494.1   0.0     2e-152  493.8   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4130  D-serine dehydratase (EC 4.3.1.1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4130  D-serine dehydratase (EC 4.3.1.18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  493.8   0.0    2e-152    2e-152      10     428 ..      17     436 ..       7     439 .. 0.94

  Alignments for each domain:
  == domain 1  score: 493.8 bits;  conditional E-value: 2e-152
                                        TIGR02035  10 dlidlkevewanpkkasl.aealkkvdlk..eqevkeaearlkrfapyiakvfpetaatkGi 68 
                                                       l +++++ w+np+++++ a al+ ++ +    + + a arl rfa ++a+vfpe aat+G+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4130  17 RLRNAQPALWTNPARQAQpAAALPALGRTisLDDTHAAAARLARFAGLLAQVFPELAATGGV 78 
                                                      5667899******9875427789998865215689999************************ PP

                                        TIGR02035  69 ieselvevaalkkklekkyqqelsGrlllkkdshlpisGsikarGGiyevlkhaeklaleaG 130
                                                      +es+l   aal  +l     +e +G l++k d+ lp++GsikarGG++evl++ae lal++G
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4130  79 VESPLLPAAALAPALGM---AEAQGSLFIKADHSLPVAGSIKARGGMHEVLEFAEGLALQHG 137
                                                      *************9986...6788************************************** PP

                                        TIGR02035 131 llkldddysklaeeefkdffsrykiavGstGnlGlsiGiisaalGfkvtvhmsadakkwkkd 192
                                                      l++   dy+ la ++ ++ + ry++avGstGnlG+siG++++alGf++tvhmsadak+wkkd
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4130 138 LVQPGGDYRALATPQAREVLGRYQVAVGSTGNLGMSIGVVASALGFQATVHMSADAKEWKKD 199
                                                      ************************************************************** PP

                                        TIGR02035 193 klrskGvtvveyesdyskaveeGrkeaeadplsyfvddeksrdlflGyavaasrlkkqldkk 254
                                                      +lr++Gv vve+  dy +av  Gr ea+++pl++fvdde+s +l+lGy+ aa  l+kql+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4130 200 RLRQRGVLVVEHTGDYERAVAAGRAEAASNPLCHFVDDEQSFSLLLGYSAAALHLQKQLAEQ 261
                                                      ************************************************************** PP

                                        TIGR02035 255 gikvdkehplfvylpcGvGGgpGGvafGlkllfgddvhvffaepthspcmllGlytGlheki 316
                                                      g+ vd+ehpl+vylpcGvGG+p G++fGl+++ g +vh+ffaep++spc l+ + +G+ e+ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4130 262 GVAVDAEHPLIVYLPCGVGGAPAGITFGLRQVLGPHVHCFFAEPVQSPCFLVQMMAGQGEHP 323
                                                      ************************************************************** PP

                                        TIGR02035 317 svqdiGidnltaadGlavgrpsGlvGrllerlldGiytvddeklydllallaesedkrleps 378
                                                      sv+d G+ n+t+adGlav r+s l   l+++ll+G++tv d++l+  l  +    + r+eps
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4130 324 SVYDWGLTNRTEADGLAVPRASLLAAELMQPLLSGVFTVADDTLFAHLVRVLDALGERIEPS 385
                                                      *********************************************9999888999******* PP

                                        TIGR02035 379 alaglaGvvrllkeeeskreaekl.iakklenavhlvwatGGkmvpeeeme 428
                                                      a ag+ G++ l+ +  ++   ++  i + l++a+hlvw+tGG +vp+ + +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4130 386 AAAGFSGPALLTGTTAGQAWLRSTgIDAVLHQATHLVWTTGGLLVPDAQYQ 436
                                                      **************9999876654267889****************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (431 nodes)
Target sequences:                          1  (450 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.77
//
[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