GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Lactobacillus shenzhenensis LY-73

Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_051999841.1 L248_RS03260 D-serine ammonia-lyase

Query= BRENDA::Q4A041
         (433 letters)



>NCBI__GCF_000469325.1:WP_051999841.1
          Length = 451

 Score =  454 bits (1167), Expect = e-132
 Identities = 226/432 (52%), Positives = 295/432 (68%), Gaps = 1/432 (0%)

Query: 3   DLATLKQDFPLIDSMQNYKPIFWENPNFRKPASL-TFTLKDMEDAAQRLERFSSYISTVF 61
           D   L   FP + +  N  P FW NP++  P    +    D+ DA  R  RF+ Y++ VF
Sbjct: 13  DKQELLTQFPALAAYANETPTFWANPHYGHPRKDDSMREADVFDAGTRFRRFAPYLAEVF 72

Query: 62  PETENNHGLIESPLKHIPFMQNTLTNIESLPIEGKLWLKCDSHLAISGSIKARGGIYEVL 121
           PET   HG+IESP+  +P ++  +         GKL++K DS L +SGSIK+RGGIYEVL
Sbjct: 73  PETAPAHGIIESPIYRLPHLEKQIAADTGTVFPGKLFMKADSELPVSGSIKSRGGIYEVL 132

Query: 122 KLAETIAMQDGDLKETADYRVLAEQKYQDLFSKYNVAVGSTGNLGLSIGIMSAKLGFKVT 181
           K AETIAM++GDL  T DYR+L   +Y+ LFSKY +AVGSTGNLGLSIGIM+A LGF+ T
Sbjct: 133 KFAETIAMREGDLAYTDDYRILDSPRYKRLFSKYEIAVGSTGNLGLSIGIMAATLGFRTT 192

Query: 182 VHMSTDARQWKKDLLRSRGVEVIEHQSDYQYAVAEGRKHAENDPTCHFVDDEGSSDLFLG 241
           VHMS DARQWKKD LR+ GV V+E+ +D+  A+  GRK AE+ P  +F+DDEGS DLF G
Sbjct: 193 VHMSADARQWKKDKLRANGVNVVEYDADFTTAITAGRKLAESQPNTYFIDDEGSKDLFFG 252

Query: 242 YTVAALRLKAQLAAENIQIDAEHPLFVYIPCGVGGGPGGVTFGLKQVFGEHVYCIFTEPT 301
           Y VAA+RL  QL    I++DA+HP+FVY+P GVGG PGGVTFGLK V G +++ IF EPT
Sbjct: 253 YAVAAIRLGKQLKDAGIKMDADHPVFVYLPAGVGGSPGGVTFGLKTVLGPNIHGIFAEPT 312

Query: 302 HAPCMLLGMMTQLHDKISVKDIGIDGNTDADGLAVARPSRLVGQIMNTLLYGIQTVSDSE 361
           H P + +GM++ L +KI+V D+GIDG T ADGLAV RPSRL G++M+TLL G  T  D +
Sbjct: 313 HMPSVTIGMISGLQEKITVYDLGIDGKTAADGLAVPRPSRLAGRVMDTLLLGSCTFPDHD 372

Query: 362 MYRYLYLLSEKEDIFIEPSAASGFAGIKSAITLAKQQGIQMNQANHIVWATGGNMVPKEE 421
           M R+   L+E+E   +EPS A G A ++ +    K+ G  +  A HI+WATGG+MVP  E
Sbjct: 373 MMRWTARLAEQEQHNVEPSGAGGLAILERSFPALKKLGYPVENATHIIWATGGSMVPAPE 432

Query: 422 MLKYVNHGKSCL 433
           M  Y+  G + L
Sbjct: 433 MADYIKTGDALL 444


Lambda     K      H
   0.318    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: 503
Number of extensions: 16
Number of successful extensions: 2
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: 433
Length of database: 451
Length adjustment: 32
Effective length of query: 401
Effective length of database: 419
Effective search space:   168019
Effective search space used:   168019
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_051999841.1 L248_RS03260 (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.2760598.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-165  537.5   0.0   1.3e-165  537.3   0.0    1.0  1  NCBI__GCF_000469325.1:WP_051999841.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000469325.1:WP_051999841.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  537.3   0.0  1.3e-165  1.3e-165       2     430 ..      18     436 ..      17     437 .. 0.97

  Alignments for each domain:
  == domain 1  score: 537.3 bits;  conditional E-value: 1.3e-165
                             TIGR02035   2 llkeplikdlidlkevewanpkkaslaealkkvdlkeqevkeaearlkrfapyiakvfpetaatkGiieselv 74 
                                           l ++p ++   +  +++wanp+      + k+ +++e++v +a  r++rfapy+a+vfpeta ++Giies++ 
  NCBI__GCF_000469325.1:WP_051999841.1  18 LTQFPALAAYANETPTFWANPHYG---HPRKDDSMREADVFDAGTRFRRFAPYLAEVFPETAPAHGIIESPIY 87 
                                           7899*****************865...8899999*************************************** PP

                             TIGR02035  75 evaalkkklekkyqqelsGrlllkkdshlpisGsikarGGiyevlkhaeklaleaGllkldddysklaeeefk 147
                                            + +l+k++ ++  + ++G+l++k ds+lp+sGsik+rGGiyevlk+ae +a+++G l  +ddy++l ++++k
  NCBI__GCF_000469325.1:WP_051999841.1  88 RLPHLEKQIAADTGTVFPGKLFMKADSELPVSGSIKSRGGIYEVLKFAETIAMREGDLAYTDDYRILDSPRYK 160
                                           ************************************************************************* PP

                             TIGR02035 148 dffsrykiavGstGnlGlsiGiisaalGfkvtvhmsadakkwkkdklrskGvtvveyesdyskaveeGrkeae 220
                                            +fs+y+iavGstGnlGlsiGi++a+lGf+ tvhmsada++wkkdklr++Gv+vvey++d+++a+  Grk ae
  NCBI__GCF_000469325.1:WP_051999841.1 161 RLFSKYEIAVGSTGNLGLSIGIMAATLGFRTTVHMSADARQWKKDKLRANGVNVVEYDADFTTAITAGRKLAE 233
                                           ************************************************************************* PP

                             TIGR02035 221 adplsyfvddeksrdlflGyavaasrlkkqldkkgikvdkehplfvylpcGvGGgpGGvafGlkllfgddvhv 293
                                           ++p++yf+dde s+dlf+Gyavaa rl kql+ +gik+d++hp+fvylp GvGG+pGGv+fGlk + g ++h 
  NCBI__GCF_000469325.1:WP_051999841.1 234 SQPNTYFIDDEGSKDLFFGYAVAAIRLGKQLKDAGIKMDADHPVFVYLPAGVGGSPGGVTFGLKTVLGPNIHG 306
                                           ************************************************************************* PP

                             TIGR02035 294 ffaepthspcmllGlytGlhekisvqdiGidnltaadGlavgrpsGlvGrllerlldGiytvddeklydllal 366
                                           +faepth p + +G+ +Gl eki+v+d+Gid++taadGlav rps l Gr+++ ll G  t  d+++ +  a 
  NCBI__GCF_000469325.1:WP_051999841.1 307 IFAEPTHMPSVTIGMISGLQEKITVYDLGIDGKTAADGLAVPRPSRLAGRVMDTLLLGSCTFPDHDMMRWTAR 379
                                           ************************************************************************* PP

                             TIGR02035 367 laesedkrlepsalaglaGvvrllkeeeskreaekliakklenavhlvwatGGkmvpeeemeay 430
                                           lae+e+  +eps   gla + r +         +kl +  +ena+h++watGG+mvp  em+ y
  NCBI__GCF_000469325.1:WP_051999841.1 380 LAEQEQHNVEPSGAGGLAILERSF------PALKKL-GYPVENATHIIWATGGSMVPAPEMADY 436
                                           ************877766544444......344444.779*********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (431 nodes)
Target sequences:                          1  (451 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 21.62
//
[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:

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:

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:

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:

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