GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Desulfitobacterium hafniense DCB-2

Align D-serine dehydratase; D-serine deaminase; DSD; EC 4.3.1.18 (characterized)
to candidate WP_193345603.1 DHAF_RS14450 D-serine ammonia-lyase

Query= SwissProt::Q8FFF4
         (442 letters)



>NCBI__GCF_000021925.1:WP_193345603.1
          Length = 444

 Score =  507 bits (1306), Expect = e-148
 Identities = 264/442 (59%), Positives = 311/442 (70%), Gaps = 5/442 (1%)

Query: 5   KMNSLIAQYPLVEDLVALKETTWFNPGTTSLAEGLP-YVGLTEQDVQDAHARLSRFAPYL 63
           K   +I   P+V+DL A +E  W NP   +  E      G++  D+ DA  RL RFAPYL
Sbjct: 4   KSPEVIPHTPVVQDLRAAREIFWINPHYRATKEFKEAQFGISLSDIHDAEERLRRFAPYL 63

Query: 64  AKAFPETAAAGGIIESELVAIPAMQKRLEKEYQQPIAGQLLLKKDSHLPISGSIKARGGI 123
           AKAFPET  A G+IES +V I  MQ  LE  Y   I G + LK D  LPISGSIKARGGI
Sbjct: 64  AKAFPETQPAQGLIESPIVPIKRMQSYLESRYGVQIPGDIWLKCDHQLPISGSIKARGGI 123

Query: 124 YEVLAHAEKLALEAGLLTLEDDYSKLLSPEFKQFFSQYSIAVGSTGNLGLSIGIMSARIG 183
           YEVL HAE+  ++ GLLT EDDY++L    F+   S Y IAVGSTGNLGLSIG+M A +G
Sbjct: 124 YEVLKHAEETLIKQGLLTREDDYARLKDSSFRDVLSHYKIAVGSTGNLGLSIGVMGAELG 183

Query: 184 FKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRT 243
           FKVTVHMSADA+ WKKA LRS GV V+EY  DY  AVEEGR+ A+ D  C FIDDENSR 
Sbjct: 184 FKVTVHMSADAKGWKKALLRSKGVEVIEYTSDYSKAVEEGRRQAEGDSRCHFIDDENSRD 243

Query: 244 LFLGYSVAGQRLKAQFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFF 303
           LFLGY+VAG RLK Q  +  R VDAD+PLFVYLPCGVGGGPGGV FGLK  F +HVHCFF
Sbjct: 244 LFLGYAVAGLRLKEQLEKLNRKVDADHPLFVYLPCGVGGGPGGVTFGLKQVFQEHVHCFF 303

Query: 304 AEPTHSPCMLLGVHTGLHDQISVQDIGIDNLTAADGLAVGRASGFVGRAMERLLDGFYTL 363
           AEPTHSPCM+LG+ TGLHD I+VQDIG+DN T ADGLAVGRAS FVG+ M  LL G +T+
Sbjct: 304 AEPTHSPCMVLGLATGLHDGIAVQDIGLDNKTEADGLAVGRASRFVGKIMAGLLSGAFTV 363

Query: 364 SDQTMYDMLGWLAQEEGIRLEPSALAGMAGSQRVC---ASVSYQQMHGFSAEQLRNATHL 420
            D  ++ +L  L   EGI+ EPSALAGMAG  R+      + Y + H    E L+  THL
Sbjct: 364 EDAELFRLLQALDHAEGIQCEPSALAGMAGPARLLLCKEGLQYIREHRLE-EGLKKGTHL 422

Query: 421 VWATGGGMVPEEEMNQYLAKGR 442
           +WATGG +VPEE M  YL++G+
Sbjct: 423 IWATGGSLVPEEVMKDYLSRGK 444


Lambda     K      H
   0.319    0.135    0.397 

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: 568
Number of extensions: 18
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: 442
Length of database: 444
Length adjustment: 32
Effective length of query: 410
Effective length of database: 412
Effective search space:   168920
Effective search space used:   168920
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_193345603.1 DHAF_RS14450 (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.727771.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.7e-204  664.3   0.0   4.2e-204  664.1   0.0    1.0  1  NCBI__GCF_000021925.1:WP_193345603.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000021925.1:WP_193345603.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  664.1   0.0  4.2e-204  4.2e-204       3     431 .]      10     440 ..       8     440 .. 0.98

  Alignments for each domain:
  == domain 1  score: 664.1 bits;  conditional E-value: 4.2e-204
                             TIGR02035   3 lkeplikdlidlkevewanpkkaslae.alkkvdlkeqevkeaearlkrfapyiakvfpetaatkGiieselv 74 
                                            ++p+++dl +++e++w+np+  +++e ++++ ++  +++++ae+rl+rfapy+ak+fpet+ ++G+ies++v
  NCBI__GCF_000021925.1:WP_193345603.1  10 PHTPVVQDLRAAREIFWINPHYRATKEfKEAQFGISLSDIHDAEERLRRFAPYLAKAFPETQPAQGLIESPIV 82 
                                           578*****************9988777357899**************************************** PP

                             TIGR02035  75 evaalkkklekkyqqelsGrlllkkdshlpisGsikarGGiyevlkhaeklaleaGllkldddysklaeeefk 147
                                            ++++++ le +y  +++G ++lk+d++lpisGsikarGGiyevlkhae+  +++Gll+ +ddy++l++++f+
  NCBI__GCF_000021925.1:WP_193345603.1  83 PIKRMQSYLESRYGVQIPGDIWLKCDHQLPISGSIKARGGIYEVLKHAEETLIKQGLLTREDDYARLKDSSFR 155
                                           ************************************************************************* PP

                             TIGR02035 148 dffsrykiavGstGnlGlsiGiisaalGfkvtvhmsadakkwkkdklrskGvtvveyesdyskaveeGrkeae 220
                                           d +s+ykiavGstGnlGlsiG+++a lGfkvtvhmsadak wkk++lrskGv+v+ey sdyskaveeGr++ae
  NCBI__GCF_000021925.1:WP_193345603.1 156 DVLSHYKIAVGSTGNLGLSIGVMGAELGFKVTVHMSADAKGWKKALLRSKGVEVIEYTSDYSKAVEEGRRQAE 228
                                           ************************************************************************* PP

                             TIGR02035 221 adplsyfvddeksrdlflGyavaasrlkkqldkkgikvdkehplfvylpcGvGGgpGGvafGlkllfgddvhv 293
                                           +d  ++f+dde+srdlflGyava+ rlk+ql+k ++kvd++hplfvylpcGvGGgpGGv+fGlk++f+++vh+
  NCBI__GCF_000021925.1:WP_193345603.1 229 GDSRCHFIDDENSRDLFLGYAVAGLRLKEQLEKLNRKVDADHPLFVYLPCGVGGGPGGVTFGLKQVFQEHVHC 301
                                           ************************************************************************* PP

                             TIGR02035 294 ffaepthspcmllGlytGlhekisvqdiGidnltaadGlavgrpsGlvGrllerlldGiytvddeklydllal 366
                                           ffaepthspcm+lGl tGlh+ i+vqdiG+dn+t+adGlavgr+s +vG+++  ll+G +tv+d +l++ll+ 
  NCBI__GCF_000021925.1:WP_193345603.1 302 FFAEPTHSPCMVLGLATGLHDGIAVQDIGLDNKTEADGLAVGRASRFVGKIMAGLLSGAFTVEDAELFRLLQA 374
                                           ************************************************************************* PP

                             TIGR02035 367 laesedkrlepsalaglaGvvrllkeeeskreaek.liakklenavhlvwatGGkmvpeeemeayl 431
                                           l++ e+++ epsalag+aG++rll  +e+ +++++ +  + l++ +hl+watGG++vpee m+ yl
  NCBI__GCF_000021925.1:WP_193345603.1 375 LDHAEGIQCEPSALAGMAGPARLLLCKEGLQYIREhRLEEGLKKGTHLIWATGGSLVPEEVMKDYL 440
                                           *******************************9876156788**********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (431 nodes)
Target sequences:                          1  (444 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: 17.04
//
[ok]

This GapMind analysis is from Apr 09 2024. 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