Alignments for a candidate for dsdA in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for dsdA in Pseudomonas benzenivorans DSM 8628

Align D-serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_090447547.1 BLS63_RS19965 D-serine ammonia-lyase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3648
         (450 letters)



>NCBI__GCF_900100495.1:WP_090447547.1
          Length = 450

 Score =  673 bits (1737), Expect = 0.0
 Identities = 329/447 (73%), Positives = 382/447 (85%)

Query: 1   MILGKTLESWYASYPLIRDLVALQETTWFNPAVAPVAESIGDVGLTAADVADASARLTRF 60
           M+LGK+L +W A YPL+ +L+AL+ET+WFNP V P +E++ DVGL+AADVADASARL RF
Sbjct: 1   MVLGKSLAAWRAEYPLLDELIALRETSWFNPGVVPASEALADVGLSAADVADASARLARF 60

Query: 61  ASYLRRAFPETECSGGIIESDILPVPHLQQLLGERYGQALQGALWLKRDSHLPISGSIKA 120
           A YL R FPET   GGIIESDIL +P LQ +L ER+G +  GALWLKRDSHLPISGSIKA
Sbjct: 61  APYLARVFPETAGQGGIIESDILALPRLQAVLSERHGLSAGGALWLKRDSHLPISGSIKA 120

Query: 121 RGGIYEVLKHAEDLALAANLLTLDDDYAVLDSDKARAFFGQYKIAVGSTGNLGMSIGIMG 180
           RGGIYEVLKHAE LALAA LL   DDY VLDSD A+AFFG+Y+IAVGSTGNLG+SIGI+ 
Sbjct: 121 RGGIYEVLKHAEGLALAAGLLKAGDDYGVLDSDAAQAFFGRYQIAVGSTGNLGLSIGIIA 180

Query: 181 AALGFQVTVHMSADARQWKKDKLRSHGVTVIEYSSDYSVAVSQGRQQAESDPACHFVDDE 240
           A LGFQ TVHMSADARQWKK++LR+HGV V+EY+SDYSVAV++GR+QA +DP CHFVDDE
Sbjct: 181 ARLGFQATVHMSADARQWKKERLRAHGVRVVEYASDYSVAVAEGRRQAAADPRCHFVDDE 240

Query: 241 NSVSLFLGYSVAAERLKKQLAAADITVDAQHPLFVYLPCGVGGAPGGVAFGLKLAFGDAV 300
           NS  LFLGY+VA ERL++QLAAA I VDA+HPLFVYLPCGVGG PGGVAFGLKLAFGDAV
Sbjct: 241 NSTHLFLGYAVAGERLRQQLAAAAIAVDAEHPLFVYLPCGVGGGPGGVAFGLKLAFGDAV 300

Query: 301 HCIFAEPTHSPCMMLGVYSGLHDEVSVQDFGIDNVTAADGLAVGRASGFVGKAMQRLLDG 360
            C+FAEPTHSPCM+LGVYSG HD +SVQDFGIDN TAADGLAVGR SGFVG+AMQRL+DG
Sbjct: 301 RCLFAEPTHSPCMLLGVYSGRHDALSVQDFGIDNRTAADGLAVGRPSGFVGRAMQRLIDG 360

Query: 361 FYTVSDEEMYSLLALMERSEGVRLEPSALAGVPGIARVQADQQGYLARARLDRQAMVQAT 420
           +YTVSDEE++  LAL+E SEG RLEPSALAG+PG+ R+  ++QGY AR  L    + +AT
Sbjct: 361 YYTVSDEELFRCLALLEASEGQRLEPSALAGMPGLVRLLGERQGYRARLGLTPARLARAT 420

Query: 421 HLVWATGGNMVPCDEMEAYLAKGRELL 447
           HLVWATGG+MVP  EM  YLA+GR+LL
Sbjct: 421 HLVWATGGSMVPEAEMAGYLARGRQLL 447


Lambda     K      H
   0.320    0.135    0.398 

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: 683
Number of extensions: 24
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: 450
Length of database: 450
Length adjustment: 33
Effective length of query: 417
Effective length of database: 417
Effective search space:   173889
Effective search space used:   173889
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_090447547.1 BLS63_RS19965 (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.19611.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-217  707.8   0.0   2.6e-217  707.6   0.0    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090447547.1  BLS63_RS19965 D-serine ammonia-l


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090447547.1  BLS63_RS19965 D-serine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  707.6   0.0  2.6e-217  2.6e-217       3     431 .]      12     440 ..      10     440 .. 0.99

  Alignments for each domain:
  == domain 1  score: 707.6 bits;  conditional E-value: 2.6e-217
                                 TIGR02035   3 lkeplikdlidlkevewanpkkaslaealkkvdlkeqevkeaearlkrfapyiakvfpetaatkGiies 71 
                                               +++pl+++li+l+e++w+np+  + +eal++v+l +++v++a+arl rfapy+a+vfpeta+ +Giies
  lcl|NCBI__GCF_900100495.1:WP_090447547.1  12 AEYPLLDELIALRETSWFNPGVVPASEALADVGLSAADVADASARLARFAPYLARVFPETAGQGGIIES 80 
                                               789****************************************************************** PP

                                 TIGR02035  72 elvevaalkkklekkyqqelsGrlllkkdshlpisGsikarGGiyevlkhaeklaleaGllkldddysk 140
                                               ++ ++ +l+  l +++     G l+lk+dshlpisGsikarGGiyevlkhae lal aGllk  ddy  
  lcl|NCBI__GCF_900100495.1:WP_090447547.1  81 DILALPRLQAVLSERHGLSAGGALWLKRDSHLPISGSIKARGGIYEVLKHAEGLALAAGLLKAGDDYGV 149
                                               ********************************************************************* PP

                                 TIGR02035 141 laeeefkdffsrykiavGstGnlGlsiGiisaalGfkvtvhmsadakkwkkdklrskGvtvveyesdys 209
                                               l ++  ++ff ry+iavGstGnlGlsiGii+a+lGf++tvhmsada++wkk++lr++Gv+vvey+sdys
  lcl|NCBI__GCF_900100495.1:WP_090447547.1 150 LDSDAAQAFFGRYQIAVGSTGNLGLSIGIIAARLGFQATVHMSADARQWKKERLRAHGVRVVEYASDYS 218
                                               ********************************************************************* PP

                                 TIGR02035 210 kaveeGrkeaeadplsyfvddeksrdlflGyavaasrlkkqldkkgikvdkehplfvylpcGvGGgpGG 278
                                               +av eGr++a+adp ++fvdde+s +lflGyava++rl++ql++++i vd+ehplfvylpcGvGGgpGG
  lcl|NCBI__GCF_900100495.1:WP_090447547.1 219 VAVAEGRRQAAADPRCHFVDDENSTHLFLGYAVAGERLRQQLAAAAIAVDAEHPLFVYLPCGVGGGPGG 287
                                               ********************************************************************* PP

                                 TIGR02035 279 vafGlkllfgddvhvffaepthspcmllGlytGlhekisvqdiGidnltaadGlavgrpsGlvGrller 347
                                               vafGlkl+fgd+v ++faepthspcmllG+y+G+h+ +svqd+Gidn+taadGlavgrpsG+vGr+++r
  lcl|NCBI__GCF_900100495.1:WP_090447547.1 288 VAFGLKLAFGDAVRCLFAEPTHSPCMLLGVYSGRHDALSVQDFGIDNRTAADGLAVGRPSGFVGRAMQR 356
                                               ********************************************************************* PP

                                 TIGR02035 348 lldGiytvddeklydllallaesedkrlepsalaglaGvvrllkeeeskreaekliakklenavhlvwa 416
                                               l+dG+ytv+de+l++ lall+ se++rlepsalag+ G+vrll e +++r + +l+ ++l++a+hlvwa
  lcl|NCBI__GCF_900100495.1:WP_090447547.1 357 LIDGYYTVSDEELFRCLALLEASEGQRLEPSALAGMPGLVRLLGERQGYRARLGLTPARLARATHLVWA 425
                                               ********************************************************************* PP

                                 TIGR02035 417 tGGkmvpeeemeayl 431
                                               tGG+mvpe em+ yl
  lcl|NCBI__GCF_900100495.1:WP_090447547.1 426 TGGSMVPEAEMAGYL 440
                                               ***********9996 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.61
//
[ok]

This GapMind analysis is from Sep 24 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