Alignments for a candidate for dsdA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for dsdA in Pseudomonas fluorescens GW456-L13

Align D-serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate PfGW456L13_3648 D-serine dehydratase (EC 4.3.1.18)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3648
          Length = 450

 Score =  891 bits (2303), Expect = 0.0
 Identities = 450/450 (100%), Positives = 450/450 (100%)

Query: 1   MILGKTLESWYASYPLIRDLVALQETTWFNPAVAPVAESIGDVGLTAADVADASARLTRF 60
           MILGKTLESWYASYPLIRDLVALQETTWFNPAVAPVAESIGDVGLTAADVADASARLTRF
Sbjct: 1   MILGKTLESWYASYPLIRDLVALQETTWFNPAVAPVAESIGDVGLTAADVADASARLTRF 60

Query: 61  ASYLRRAFPETECSGGIIESDILPVPHLQQLLGERYGQALQGALWLKRDSHLPISGSIKA 120
           ASYLRRAFPETECSGGIIESDILPVPHLQQLLGERYGQALQGALWLKRDSHLPISGSIKA
Sbjct: 61  ASYLRRAFPETECSGGIIESDILPVPHLQQLLGERYGQALQGALWLKRDSHLPISGSIKA 120

Query: 121 RGGIYEVLKHAEDLALAANLLTLDDDYAVLDSDKARAFFGQYKIAVGSTGNLGMSIGIMG 180
           RGGIYEVLKHAEDLALAANLLTLDDDYAVLDSDKARAFFGQYKIAVGSTGNLGMSIGIMG
Sbjct: 121 RGGIYEVLKHAEDLALAANLLTLDDDYAVLDSDKARAFFGQYKIAVGSTGNLGMSIGIMG 180

Query: 181 AALGFQVTVHMSADARQWKKDKLRSHGVTVIEYSSDYSVAVSQGRQQAESDPACHFVDDE 240
           AALGFQVTVHMSADARQWKKDKLRSHGVTVIEYSSDYSVAVSQGRQQAESDPACHFVDDE
Sbjct: 181 AALGFQVTVHMSADARQWKKDKLRSHGVTVIEYSSDYSVAVSQGRQQAESDPACHFVDDE 240

Query: 241 NSVSLFLGYSVAAERLKKQLAAADITVDAQHPLFVYLPCGVGGAPGGVAFGLKLAFGDAV 300
           NSVSLFLGYSVAAERLKKQLAAADITVDAQHPLFVYLPCGVGGAPGGVAFGLKLAFGDAV
Sbjct: 241 NSVSLFLGYSVAAERLKKQLAAADITVDAQHPLFVYLPCGVGGAPGGVAFGLKLAFGDAV 300

Query: 301 HCIFAEPTHSPCMMLGVYSGLHDEVSVQDFGIDNVTAADGLAVGRASGFVGKAMQRLLDG 360
           HCIFAEPTHSPCMMLGVYSGLHDEVSVQDFGIDNVTAADGLAVGRASGFVGKAMQRLLDG
Sbjct: 301 HCIFAEPTHSPCMMLGVYSGLHDEVSVQDFGIDNVTAADGLAVGRASGFVGKAMQRLLDG 360

Query: 361 FYTVSDEEMYSLLALMERSEGVRLEPSALAGVPGIARVQADQQGYLARARLDRQAMVQAT 420
           FYTVSDEEMYSLLALMERSEGVRLEPSALAGVPGIARVQADQQGYLARARLDRQAMVQAT
Sbjct: 361 FYTVSDEEMYSLLALMERSEGVRLEPSALAGVPGIARVQADQQGYLARARLDRQAMVQAT 420

Query: 421 HLVWATGGNMVPCDEMEAYLAKGRELLAKG 450
           HLVWATGGNMVPCDEMEAYLAKGRELLAKG
Sbjct: 421 HLVWATGGNMVPCDEMEAYLAKGRELLAKG 450


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: 795
Number of extensions: 17
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 PfGW456L13_3648 (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.8777.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.6e-221  721.5   0.0   1.8e-221  721.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3648  D-serine dehydratase (EC 4.3.1.1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3648  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 !  721.4   0.0  1.8e-221  1.8e-221       3     431 .]      12     440 ..      10     440 .. 0.99

  Alignments for each domain:
  == domain 1  score: 721.4 bits;  conditional E-value: 1.8e-221
                                               TIGR02035   3 lkeplikdlidlkevewanpkkaslaealkkvdlkeqevkeaearlkrfapyiak 57 
                                                             + +pli+dl++l+e++w+np+ a++ae++ +v+l++++v++a+arl rfa y+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3648  12 ASYPLIRDLVALQETTWFNPAVAPVAESIGDVGLTAADVADASARLTRFASYLRR 66 
                                                             789**************************************************** PP

                                               TIGR02035  58 vfpetaatkGiieselvevaalkkklekkyqqelsGrlllkkdshlpisGsikar 112
                                                             +fpet+ ++Giies++  v +l++ l ++y q l+G l+lk+dshlpisGsikar
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3648  67 AFPETECSGGIIESDILPVPHLQQLLGERYGQALQGALWLKRDSHLPISGSIKAR 121
                                                             ******************************************************* PP

                                               TIGR02035 113 GGiyevlkhaeklaleaGllkldddysklaeeefkdffsrykiavGstGnlGlsi 167
                                                             GGiyevlkhae+lal a ll+ldddy+ l +++ ++ff +ykiavGstGnlG+si
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3648 122 GGIYEVLKHAEDLALAANLLTLDDDYAVLDSDKARAFFGQYKIAVGSTGNLGMSI 176
                                                             ******************************************************* PP

                                               TIGR02035 168 GiisaalGfkvtvhmsadakkwkkdklrskGvtvveyesdyskaveeGrkeaead 222
                                                             Gi++aalGf+vtvhmsada++wkkdklrs+Gvtv+ey sdys+av +Gr++ae+d
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3648 177 GIMGAALGFQVTVHMSADARQWKKDKLRSHGVTVIEYSSDYSVAVSQGRQQAESD 231
                                                             ******************************************************* PP

                                               TIGR02035 223 plsyfvddeksrdlflGyavaasrlkkqldkkgikvdkehplfvylpcGvGGgpG 277
                                                             p ++fvdde+s +lflGy+vaa+rlkkql++++i+vd++hplfvylpcGvGG+pG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3648 232 PACHFVDDENSVSLFLGYSVAAERLKKQLAAADITVDAQHPLFVYLPCGVGGAPG 286
                                                             ******************************************************* PP

                                               TIGR02035 278 GvafGlkllfgddvhvffaepthspcmllGlytGlhekisvqdiGidnltaadGl 332
                                                             GvafGlkl+fgd+vh++faepthspcm+lG+y+Glh+++svqd+Gidn taadGl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3648 287 GVAFGLKLAFGDAVHCIFAEPTHSPCMMLGVYSGLHDEVSVQDFGIDNVTAADGL 341
                                                             ******************************************************* PP

                                               TIGR02035 333 avgrpsGlvGrllerlldGiytvddeklydllallaesedkrlepsalaglaGvv 387
                                                             avgr+sG+vG++++rlldG+ytv+de++y+llal+++se++rlepsalag+ G++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3648 342 AVGRASGFVGKAMQRLLDGFYTVSDEEMYSLLALMERSEGVRLEPSALAGVPGIA 396
                                                             ******************************************************* PP

                                               TIGR02035 388 rllkeeeskreaekliakklenavhlvwatGGkmvpeeemeayl 431
                                                             r+ + ++++  + +l  + + +a+hlvwatGG+mvp +emeayl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3648 397 RVQADQQGYLARARLDRQAMVQATHLVWATGGNMVPCDEMEAYL 440
                                                             ******************************************96 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.72
//
[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