Alignments for a candidate for dsdA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for dsdA in Cupriavidus basilensis 4G11

Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate RR42_RS28450 RR42_RS28450 serine dehydratase

Query= BRENDA::Q9HYN9
         (448 letters)



>FitnessBrowser__Cup4G11:RR42_RS28450
          Length = 457

 Score =  409 bits (1051), Expect = e-118
 Identities = 228/438 (52%), Positives = 281/438 (64%), Gaps = 14/438 (3%)

Query: 18  ADLIALRPSEWFNPAIA---PSAEALADVGLGAADVADASARLQRFAPLIARLFPETAAS 74
           A L A  P  W NPA A   P  +A  +  +  ADV  A AR  RFAPL++ LFPE A +
Sbjct: 23  ASLAAATPLLWCNPARAVTPPPVQAAGEHSISLADVEAAQARFARFAPLLSALFPELAGT 82

Query: 75  GGIIESDLVEVATFHDALRQHYAAELPGRLWLKRDSHLPISGSIKARGGIYEVLAHAERL 134
            G+IES LV V +   AL   ++    GRLW+K D  LP++GSIKARGGI+EVL  AE L
Sbjct: 83  HGVIESPLVAVPSMQTALGLPHSQ---GRLWVKADHSLPVAGSIKARGGIHEVLEFAENL 139

Query: 135 ALEHGLVGLD----DDYSRLAEADCRAFFARHRIAVGSTGNLGLSIGIIGAALGFQASVH 190
           AL HGLVG      + Y  L E   RA F R+++AVGSTGNLGLSIG++ +ALGF+A+VH
Sbjct: 140 ALRHGLVGPGRNEPEHYLALREPAARALFGRYQVAVGSTGNLGLSIGVMASALGFRAAVH 199

Query: 191 MSADARQWKKDKLRAHGVTVVEYASDYSVAVEQGRREAAGDPYTHFVDDENSRDLFLGYA 250
           MS+DA+ WKK +LR  GV VVE+A DY  AV  GRR+A  D +T+FVDDE S  L LGY+
Sbjct: 200 MSSDAKAWKKARLRNRGVEVVEHAGDYEDAVAAGRRQAQQDEFTYFVDDERSLSLLLGYS 259

Query: 251 VAAERLRGQLDAAGIRVDSEHPLFVHLPCGVGGGPGGVAFGLKLAFGDAVHCLFAEPTHS 310
            AA  LR QL A  IRVD+EHPLFV+LPCGVGG P G+ FG++  FG  VHC+FAEP  S
Sbjct: 260 AAALHLRQQLAAHAIRVDAEHPLFVYLPCGVGGAPAGITFGMRQLFGPHVHCVFAEPVQS 319

Query: 311 PCMFLGVYTGRHEQVSVQDFGIDNRTAADGLAVGRPSGFVGRAMQRLLDGYYTVDDDELF 370
           PC  + +  G     SV DFG+ N T ADGLAV R S      M+ LL G +TV DD LF
Sbjct: 320 PCFLVQMMAGAGNP-SVYDFGLSNSTQADGLAVPRASELAAGVMRPLLSGVFTVADDTLF 378

Query: 371 RLLALLERSQGIRLEPSALAGATGIARVTREPQG--YRERMGLTSARLANATHLVWATGG 428
             LAL  R+QG+R+EPSA AG +G   +   P G  Y  R  L  A +  ATHLVW TGG
Sbjct: 379 EHLALAWRTQGLRIEPSAAAGFSGPRMLCESPAGRDYLARHQL-EAMMPQATHLVWTTGG 437

Query: 429 GMVPETEMRAYLERGRSL 446
             VP  E + +L++  +L
Sbjct: 438 LFVPPAEYQGFLDKAAAL 455


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: 580
Number of extensions: 26
Number of successful extensions: 6
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: 457
Length adjustment: 33
Effective length of query: 415
Effective length of database: 424
Effective search space:   175960
Effective search space used:   175960
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 RR42_RS28450 RR42_RS28450 (serine dehydratase)
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.4993.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-155  503.6   0.0   2.5e-155  503.4   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS28450  RR42_RS28450 serine dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS28450  RR42_RS28450 serine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  503.4   0.0  2.5e-155  2.5e-155      10     430 ..      24     448 ..      17     449 .. 0.94

  Alignments for each domain:
  == domain 1  score: 503.4 bits;  conditional E-value: 2.5e-155
                                 TIGR02035  10 dlidlkevewanpkkaslaealkkvdlke...qevkeaearlkrfapyiakvfpetaatkGiieselve 75 
                                                l ++ +  w np++a +  +++ ++++    ++v+ a+ar+ rfap+++ +fpe a+t+G+ies+lv+
  lcl|FitnessBrowser__Cup4G11:RR42_RS28450  24 SLAAATPLLWCNPARAVTPPPVQAAGEHSislADVEAAQARFARFAPLLSALFPELAGTHGVIESPLVA 92 
                                               67889999******9988877777776552227888899****************************** PP

                                 TIGR02035  76 vaalkkklekkyqqelsGrlllkkdshlpisGsikarGGiyevlkhaeklaleaGll....kldddysk 140
                                               v +++ +l   +    +Grl++k d+ lp++GsikarGGi+evl++ae+lal++Gl+    ++ + y  
  lcl|FitnessBrowser__Cup4G11:RR42_RS28450  93 VPSMQTALGLPHS---QGRLWVKADHSLPVAGSIKARGGIHEVLEFAENLALRHGLVgpgrNEPEHYLA 158
                                               ********98776...5***************************************9444346789*** PP

                                 TIGR02035 141 laeeefkdffsrykiavGstGnlGlsiGiisaalGfkvtvhmsadakkwkkdklrskGvtvveyesdys 209
                                               l e+  +++f ry++avGstGnlGlsiG++++alGf+++vhms+dak+wkk++lr++Gv+vve++ dy 
  lcl|FitnessBrowser__Cup4G11:RR42_RS28450 159 LREPAARALFGRYQVAVGSTGNLGLSIGVMASALGFRAAVHMSSDAKAWKKARLRNRGVEVVEHAGDYE 227
                                               ********************************************************************* PP

                                 TIGR02035 210 kaveeGrkeaeadplsyfvddeksrdlflGyavaasrlkkqldkkgikvdkehplfvylpcGvGGgpGG 278
                                                av  Gr++a++d ++yfvdde+s +l+lGy+ aa  l++ql++++i+vd+ehplfvylpcGvGG+p G
  lcl|FitnessBrowser__Cup4G11:RR42_RS28450 228 DAVAAGRRQAQQDEFTYFVDDERSLSLLLGYSAAALHLRQQLAAHAIRVDAEHPLFVYLPCGVGGAPAG 296
                                               ********************************************************************* PP

                                 TIGR02035 279 vafGlkllfgddvhvffaepthspcmllGlytGlhekisvqdiGidnltaadGlavgrpsGlvGrller 347
                                               ++fG+++lfg +vh++faep++spc l+ + +G  +  sv+d+G+ n t+adGlav r+s l   ++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS28450 297 ITFGMRQLFGPHVHCVFAEPVQSPCFLVQMMAGAGN-PSVYDFGLSNSTQADGLAVPRASELAAGVMRP 364
                                               *********************************876.6******************************* PP

                                 TIGR02035 348 lldGiytvddeklydllallaesedkrlepsalaglaGvvrllkeeeskreaekli.akklenavhlvw 415
                                               ll+G++tv d++l++ lal  ++++ r+epsa ag+ G+  l++++ ++ +  ++   + + +a+hlvw
  lcl|FitnessBrowser__Cup4G11:RR42_RS28450 365 LLSGVFTVADDTLFEHLALAWRTQGLRIEPSAAAGFSGPRMLCESPAGRDYLARHQlEAMMPQATHLVW 433
                                               **************************************************9876651567889****** PP

                                 TIGR02035 416 atGGkmvpeeemeay 430
                                               +tGG  vp  e + +
  lcl|FitnessBrowser__Cup4G11:RR42_RS28450 434 TTGGLFVPPAEYQGF 448
                                               ********9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (431 nodes)
Target sequences:                          1  (457 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: 10.79
//
[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