Aligments for a candidate for dsdA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments for a candidate for dsdA in Escherichia coli BW25113

Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate 16471 b2366 D-serine dehydratase (NCBI)

Query= BRENDA::P00926
         (442 letters)



>FitnessBrowser__Keio:16471
          Length = 442

 Score =  884 bits (2284), Expect = 0.0
 Identities = 442/442 (100%), Positives = 442/442 (100%)

Query: 1   MENAKMNSLIAQYPLVKDLVALKETTWFNPGTTSLAEGLPYVGLTEQDVQDAHARLSRFA 60
           MENAKMNSLIAQYPLVKDLVALKETTWFNPGTTSLAEGLPYVGLTEQDVQDAHARLSRFA
Sbjct: 1   MENAKMNSLIAQYPLVKDLVALKETTWFNPGTTSLAEGLPYVGLTEQDVQDAHARLSRFA 60

Query: 61  PYLAKAFPETAATGGIIESELVAIPAMQKRLEKEYQQPISGQLLLKKDSHLPISGSIKAR 120
           PYLAKAFPETAATGGIIESELVAIPAMQKRLEKEYQQPISGQLLLKKDSHLPISGSIKAR
Sbjct: 61  PYLAKAFPETAATGGIIESELVAIPAMQKRLEKEYQQPISGQLLLKKDSHLPISGSIKAR 120

Query: 121 GGIYEVLAHAEKLALEAGLLTLDDDYSKLLSPEFKQFFSQYSIAVGSTGNLGLSIGIMSA 180
           GGIYEVLAHAEKLALEAGLLTLDDDYSKLLSPEFKQFFSQYSIAVGSTGNLGLSIGIMSA
Sbjct: 121 GGIYEVLAHAEKLALEAGLLTLDDDYSKLLSPEFKQFFSQYSIAVGSTGNLGLSIGIMSA 180

Query: 181 RIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDEN 240
           RIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDEN
Sbjct: 181 RIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDEN 240

Query: 241 SRTLFLGYSVAGQRLKAQFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVH 300
           SRTLFLGYSVAGQRLKAQFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVH
Sbjct: 241 SRTLFLGYSVAGQRLKAQFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVH 300

Query: 301 CFFAEPTHSPCMLLGVHTGLHDQISVQDIGIDNLTAADGLAVGRASGFVGRAMERLLDGF 360
           CFFAEPTHSPCMLLGVHTGLHDQISVQDIGIDNLTAADGLAVGRASGFVGRAMERLLDGF
Sbjct: 301 CFFAEPTHSPCMLLGVHTGLHDQISVQDIGIDNLTAADGLAVGRASGFVGRAMERLLDGF 360

Query: 361 YTLSDQTMYDMLGWLAQEEGIRLEPSALAGMAGPQRVCASVSYQQMHGFSAEQLRNTTHL 420
           YTLSDQTMYDMLGWLAQEEGIRLEPSALAGMAGPQRVCASVSYQQMHGFSAEQLRNTTHL
Sbjct: 361 YTLSDQTMYDMLGWLAQEEGIRLEPSALAGMAGPQRVCASVSYQQMHGFSAEQLRNTTHL 420

Query: 421 VWATGGGMVPEEEMNQYLAKGR 442
           VWATGGGMVPEEEMNQYLAKGR
Sbjct: 421 VWATGGGMVPEEEMNQYLAKGR 442


Lambda     K      H
   0.319    0.135    0.399 

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: 782
Number of extensions: 6
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: 442
Length of database: 442
Length adjustment: 32
Effective length of query: 410
Effective length of database: 410
Effective search space:   168100
Effective search space used:   168100
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 16471 b2366 (D-serine dehydratase (NCBI))
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.26569.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   9.9e-250  814.5   0.0   1.1e-249  814.3   0.0    1.0  1  lcl|FitnessBrowser__Keio:16471  b2366 D-serine dehydratase (NCBI


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16471  b2366 D-serine dehydratase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  814.3   0.0  1.1e-249  1.1e-249       1     431 []       9     438 ..       9     438 .. 1.00

  Alignments for each domain:
  == domain 1  score: 814.3 bits;  conditional E-value: 1.1e-249
                       TIGR02035   1 lllkeplikdlidlkevewanpkkaslaealkkvdlkeqevkeaearlkrfapyiakvfpetaatkGiieselvevaal 79 
                                     l++++pl+kdl++lke++w+np+++slae l++v+l+eq+v++a+arl+rfapy+ak+fpetaat+Giieselv++ a+
  lcl|FitnessBrowser__Keio:16471   9 LIAQYPLVKDLVALKETTWFNPGTTSLAEGLPYVGLTEQDVQDAHARLSRFAPYLAKAFPETAATGGIIESELVAIPAM 87 
                                     589**************************************************************************** PP

                       TIGR02035  80 kkklekkyqqelsGrlllkkdshlpisGsikarGGiyevlkhaeklaleaGllkldddysklaeeefkdffsrykiavG 158
                                     +k+lek+yqq++sG+lllkkdshlpisGsikarGGiyevl+haeklaleaGll+ldddyskl+++efk+ffs+y+iavG
  lcl|FitnessBrowser__Keio:16471  88 QKRLEKEYQQPISGQLLLKKDSHLPISGSIKARGGIYEVLAHAEKLALEAGLLTLDDDYSKLLSPEFKQFFSQYSIAVG 166
                                     ******************************************************************************* PP

                       TIGR02035 159 stGnlGlsiGiisaalGfkvtvhmsadakkwkkdklrskGvtvveyesdyskaveeGrkeaeadplsyfvddeksrdlf 237
                                     stGnlGlsiGi+sa++Gfkvtvhmsada++wkk+klrs+Gvtvveye+dy++aveeGrk+a++dp+++f+dde+sr+lf
  lcl|FitnessBrowser__Keio:16471 167 STGNLGLSIGIMSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLF 245
                                     ******************************************************************************* PP

                       TIGR02035 238 lGyavaasrlkkqldkkgikvdkehplfvylpcGvGGgpGGvafGlkllfgddvhvffaepthspcmllGlytGlheki 316
                                     lGy+va++rlk+q++++g++vd+++plfvylpcGvGGgpGGvafGlkl+fgd+vh+ffaepthspcmllG++tGlh++i
  lcl|FitnessBrowser__Keio:16471 246 LGYSVAGQRLKAQFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGVHTGLHDQI 324
                                     ******************************************************************************* PP

                       TIGR02035 317 svqdiGidnltaadGlavgrpsGlvGrllerlldGiytvddeklydllallaesedkrlepsalaglaGvvrllkeees 395
                                     svqdiGidnltaadGlavgr+sG+vGr++erlldG+yt++d+++yd+l +la++e++rlepsalag+aG++r++++  s
  lcl|FitnessBrowser__Keio:16471 325 SVQDIGIDNLTAADGLAVGRASGFVGRAMERLLDGFYTLSDQTMYDMLGWLAQEEGIRLEPSALAGMAGPQRVCAS-VS 402
                                     ***************************************************************************9.9* PP

                       TIGR02035 396 kreaekliakklenavhlvwatGGkmvpeeemeayl 431
                                     ++++++++a++l+n++hlvwatGG+mvpeeem++yl
  lcl|FitnessBrowser__Keio:16471 403 YQQMHGFSAEQLRNTTHLVWATGGGMVPEEEMNQYL 438
                                     **********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (431 nodes)
Target sequences:                          1  (442 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: 7.78
//
[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, or view the source code.

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