Alignments for a candidate for dsdA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for dsdA in Pseudomonas fluorescens FW300-N2E3

Align D-serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate AO353_25210 AO353_25210 D-serine dehydratase

Query= reanno::pseudo3_N2E3:AO353_25210
         (450 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25210
          Length = 450

 Score =  897 bits (2318), Expect = 0.0
 Identities = 450/450 (100%), Positives = 450/450 (100%)

Query: 1   MIQGKTLDAWYESHPIIKELVSLQEITWFNPAIASVSIALGDVGLNHNDVKDASERLRRF 60
           MIQGKTLDAWYESHPIIKELVSLQEITWFNPAIASVSIALGDVGLNHNDVKDASERLRRF
Sbjct: 1   MIQGKTLDAWYESHPIIKELVSLQEITWFNPAIASVSIALGDVGLNHNDVKDASERLRRF 60

Query: 61  APYIAKVFPETAAADGIIESGIQPLKKFQQRLLSEAGLPGVGSLWLKKDSDLPISGSIKA 120
           APYIAKVFPETAAADGIIESGIQPLKKFQQRLLSEAGLPGVGSLWLKKDSDLPISGSIKA
Sbjct: 61  APYIAKVFPETAAADGIIESGIQPLKKFQQRLLSEAGLPGVGSLWLKKDSDLPISGSIKA 120

Query: 121 RGGIHEVLKHAEDLALQAGLIKLDDNYEALASDSALEFFSRYKIAVGSTGNLGLSIGIMS 180
           RGGIHEVLKHAEDLALQAGLIKLDDNYEALASDSALEFFSRYKIAVGSTGNLGLSIGIMS
Sbjct: 121 RGGIHEVLKHAEDLALQAGLIKLDDNYEALASDSALEFFSRYKIAVGSTGNLGLSIGIMS 180

Query: 181 AKLGFQATVHMSSDARQWKKDKLRASGVTVVEYESDYSVAVENGRLQAEKDPACYFIDDE 240
           AKLGFQATVHMSSDARQWKKDKLRASGVTVVEYESDYSVAVENGRLQAEKDPACYFIDDE
Sbjct: 181 AKLGFQATVHMSSDARQWKKDKLRASGVTVVEYESDYSVAVENGRLQAEKDPACYFIDDE 240

Query: 241 NSPHLFLGYAVAAERLARQFEFAGVRVDADHPLFVYLPCGVGGGPGGVAFGLKLAFGDAV 300
           NSPHLFLGYAVAAERLARQFEFAGVRVDADHPLFVYLPCGVGGGPGGVAFGLKLAFGDAV
Sbjct: 241 NSPHLFLGYAVAAERLARQFEFAGVRVDADHPLFVYLPCGVGGGPGGVAFGLKLAFGDAV 300

Query: 301 HCVFAEPTHSPCMMLGVYTGLHDEVSVQEFGIDNVTAADGLAVGRPSGFVGKAMQRLIDG 360
           HCVFAEPTHSPCMMLGVYTGLHDEVSVQEFGIDNVTAADGLAVGRPSGFVGKAMQRLIDG
Sbjct: 301 HCVFAEPTHSPCMMLGVYTGLHDEVSVQEFGIDNVTAADGLAVGRPSGFVGKAMQRLIDG 360

Query: 361 YYTVTDEELYRLMFLAHELENVKLEPSALAGAPGVVRVLNDEKYLERIGVSTAKLANATH 420
           YYTVTDEELYRLMFLAHELENVKLEPSALAGAPGVVRVLNDEKYLERIGVSTAKLANATH
Sbjct: 361 YYTVTDEELYRLMFLAHELENVKLEPSALAGAPGVVRVLNDEKYLERIGVSTAKLANATH 420

Query: 421 LIWGTGGSMVPAAEFATYLDKGRALQHPAQ 450
           LIWGTGGSMVPAAEFATYLDKGRALQHPAQ
Sbjct: 421 LIWGTGGSMVPAAEFATYLDKGRALQHPAQ 450


Lambda     K      H
   0.319    0.136    0.402 

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: 870
Number of extensions: 30
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate AO353_25210 AO353_25210 (D-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.20444.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.4e-211  688.8   0.0   1.6e-211  688.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25210  AO353_25210 D-serine dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_25210  AO353_25210 D-serine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  688.6   0.0  1.6e-211  1.6e-211       4     431 .]      13     439 ..      10     439 .. 0.99

  Alignments for each domain:
  == domain 1  score: 688.6 bits;  conditional E-value: 1.6e-211
                                     TIGR02035   4 keplikdlidlkevewanpkkaslaealkkvdlkeqevkeaearlkrfapyiakvfpetaatkGi 68 
                                                    +p+ik+l++l+e++w+np++as++ al +v+l++++vk+a++rl+rfapyiakvfpetaa+ Gi
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25210  13 SHPIIKELVSLQEITWFNPAIASVSIALGDVGLNHNDVKDASERLRRFAPYIAKVFPETAAADGI 77 
                                                   58*************************************************************** PP

                                     TIGR02035  69 ieselvevaalkkklekkyqqelsGrlllkkdshlpisGsikarGGiyevlkhaeklaleaGllk 133
                                                   ies +  +++++++l  +   +  G l+lkkds+lpisGsikarGGi+evlkhae+lal+aGl+k
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25210  78 IESGIQPLKKFQQRLLSEAGLPGVGSLWLKKDSDLPISGSIKARGGIHEVLKHAEDLALQAGLIK 142
                                                   ***************************************************************** PP

                                     TIGR02035 134 ldddysklaeeefkdffsrykiavGstGnlGlsiGiisaalGfkvtvhmsadakkwkkdklrskG 198
                                                   ldd+y  la+++  +ffsrykiavGstGnlGlsiGi+sa+lGf++tvhms+da++wkkdklr+ G
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25210 143 LDDNYEALASDSALEFFSRYKIAVGSTGNLGLSIGIMSAKLGFQATVHMSSDARQWKKDKLRASG 207
                                                   ***************************************************************** PP

                                     TIGR02035 199 vtvveyesdyskaveeGrkeaeadplsyfvddeksrdlflGyavaasrlkkqldkkgikvdkehp 263
                                                   vtvveyesdys+ave+Gr +ae+dp +yf+dde+s +lflGyavaa+rl  q++ +g++vd++hp
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25210 208 VTVVEYESDYSVAVENGRLQAEKDPACYFIDDENSPHLFLGYAVAAERLARQFEFAGVRVDADHP 272
                                                   ***************************************************************** PP

                                     TIGR02035 264 lfvylpcGvGGgpGGvafGlkllfgddvhvffaepthspcmllGlytGlhekisvqdiGidnlta 328
                                                   lfvylpcGvGGgpGGvafGlkl+fgd+vh++faepthspcm+lG+ytGlh+++svq++Gidn ta
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25210 273 LFVYLPCGVGGGPGGVAFGLKLAFGDAVHCVFAEPTHSPCMMLGVYTGLHDEVSVQEFGIDNVTA 337
                                                   ***************************************************************** PP

                                     TIGR02035 329 adGlavgrpsGlvGrllerlldGiytvddeklydllallaesedkrlepsalaglaGvvrllkee 393
                                                   adGlavgrpsG+vG++++rl+dG+ytv de+ly+l+ l +e e+++lepsalag+ Gvvr+l+  
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25210 338 ADGLAVGRPSGFVGKAMQRLIDGYYTVTDEELYRLMFLAHELENVKLEPSALAGAPGVVRVLND- 401
                                                   **************************************************************98. PP

                                     TIGR02035 394 eskreaekliakklenavhlvwatGGkmvpeeemeayl 431
                                                   e + e+ +++++kl+na+hl+w+tGG+mvp  e ++yl
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25210 402 EKYLERIGVSTAKLANATHLIWGTGGSMVPAAEFATYL 439
                                                   6788899999************************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.49
//
[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