Alignments for a candidate for dsdA in Thauera aminoaromatica S2

GapMind for catabolism of small carbon sources

Alignments for a candidate for dsdA in Thauera aminoaromatica S2

Align D-serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_004306148.1 C665_RS08970 D-serine ammonia-lyase

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



>NCBI__GCF_000310185.1:WP_004306148.1
          Length = 456

 Score =  695 bits (1794), Expect = 0.0
 Identities = 347/455 (76%), Positives = 392/455 (86%), Gaps = 6/455 (1%)

Query: 1   MIQGKTLDAWYESHPIIKELVSLQEITWFNPAIASVSIALGDVGLNHNDVKDASERLRRF 60
           MI GK+L+AW  SHP+I++LV+L+E +WFNP IA  + AL DVGL  +DV DAS RL+RF
Sbjct: 1   MIHGKSLEAWCASHPLIRDLVALRETSWFNPGIAPAATALADVGLGADDVADASARLQRF 60

Query: 61  APYIAKVFPETAAADGIIESGIQPLKKFQQRLLSEAG------LPGVGSLWLKKDSDLPI 114
           APYIAKVFPETAAA GIIES I PL K Q+RLL EAG      LP  G+LWLK D+ LPI
Sbjct: 61  APYIAKVFPETAAAGGIIESDIVPLPKLQRRLLEEAGKTGEAQLPAAGALWLKTDNALPI 120

Query: 115 SGSIKARGGIHEVLKHAEDLALQAGLIKLDDNYEALASDSALEFFSRYKIAVGSTGNLGL 174
           SGSIKARGGIHEVL HAE LALQAGLI+  D+Y ALASDSA  FF R++IAVGSTGNLGL
Sbjct: 121 SGSIKARGGIHEVLWHAERLALQAGLIREGDDYAALASDSAHAFFGRHRIAVGSTGNLGL 180

Query: 175 SIGIMSAKLGFQATVHMSSDARQWKKDKLRASGVTVVEYESDYSVAVENGRLQAEKDPAC 234
           SIGIMSAKLGFQATVHMS+DARQWKKD+LRASGVTVVE+ SDYSVAVE GR +A  DPAC
Sbjct: 181 SIGIMSAKLGFQATVHMSADARQWKKDRLRASGVTVVEHASDYSVAVEQGRREAASDPAC 240

Query: 235 YFIDDENSPHLFLGYAVAAERLARQFEFAGVRVDADHPLFVYLPCGVGGGPGGVAFGLKL 294
           +F+DDENSP LFLGYAVAAERLA Q + AGVRVDA+HPLFVYLPCGVGGGPGGVAFGLK 
Sbjct: 241 HFVDDENSPQLFLGYAVAAERLAGQLQRAGVRVDAEHPLFVYLPCGVGGGPGGVAFGLKR 300

Query: 295 AFGDAVHCVFAEPTHSPCMMLGVYTGLHDEVSVQEFGIDNVTAADGLAVGRPSGFVGKAM 354
            FGDAVHC+FAEPTHSPCM+LGVYTGLHD+VSVQ+FGIDNVTAADGLAVGRPSGFVGKAM
Sbjct: 301 VFGDAVHCIFAEPTHSPCMLLGVYTGLHDQVSVQDFGIDNVTAADGLAVGRPSGFVGKAM 360

Query: 355 QRLIDGYYTVTDEELYRLMFLAHELENVKLEPSALAGAPGVVRVLNDEKYLERIGVSTAK 414
           QRLIDGYYTV+DE L+RL+ LAH+ E ++LEPSALAG PG+V VL D  YL+RIGV+ A+
Sbjct: 361 QRLIDGYYTVSDEALFRLLALAHDDEGLRLEPSALAGVPGMVCVLRDAAYLDRIGVTPAR 420

Query: 415 LANATHLIWGTGGSMVPAAEFATYLDKGRALQHPA 449
            A ATHL+WGTGGSMVP +EFA ++DKGRALQ P+
Sbjct: 421 FARATHLVWGTGGSMVPDSEFAAHVDKGRALQRPS 455


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: 735
Number of extensions: 30
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: 450
Length of database: 456
Length adjustment: 33
Effective length of query: 417
Effective length of database: 423
Effective search space:   176391
Effective search space used:   176391
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 WP_004306148.1 C665_RS08970 (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.21417.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-210  685.2   0.0   1.9e-210  685.1   0.0    1.0  1  lcl|NCBI__GCF_000310185.1:WP_004306148.1  C665_RS08970 D-serine ammonia-ly


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000310185.1:WP_004306148.1  C665_RS08970 D-serine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  685.1   0.0  1.9e-210  1.9e-210       2     429 ..      11     443 ..      10     445 .. 0.97

  Alignments for each domain:
  == domain 1  score: 685.1 bits;  conditional E-value: 1.9e-210
                                 TIGR02035   2 llkeplikdlidlkevewanpkkaslaealkkvdlkeqevkeaearlkrfapyiakvfpetaatkGiie 70 
                                                + +pli+dl++l+e++w+np++a+ a al++v+l + +v++a+arl+rfapyiakvfpetaa++Giie
  lcl|NCBI__GCF_000310185.1:WP_004306148.1  11 CASHPLIRDLVALRETSWFNPGIAPAATALADVGLGADDVADASARLQRFAPYIAKVFPETAAAGGIIE 79 
                                               5789***************************************************************** PP

                                 TIGR02035  71 selvevaalkkklek......kyqqelsGrlllkkdshlpisGsikarGGiyevlkhaeklaleaGllk 133
                                               s++v + +l+ +l +      + q + +G l+lk+d+ lpisGsikarGGi+evl hae+lal+aGl++
  lcl|NCBI__GCF_000310185.1:WP_004306148.1  80 SDIVPLPKLQRRLLEeagktgEAQLPAAGALWLKTDNALPISGSIKARGGIHEVLWHAERLALQAGLIR 148
                                               **********998541122223466788***************************************** PP

                                 TIGR02035 134 ldddysklaeeefkdffsrykiavGstGnlGlsiGiisaalGfkvtvhmsadakkwkkdklrskGvtvv 202
                                               + ddy+ la+++ ++ff r++iavGstGnlGlsiGi+sa+lGf++tvhmsada++wkkd+lr+ Gvtvv
  lcl|NCBI__GCF_000310185.1:WP_004306148.1 149 EGDDYAALASDSAHAFFGRHRIAVGSTGNLGLSIGIMSAKLGFQATVHMSADARQWKKDRLRASGVTVV 217
                                               ********************************************************************* PP

                                 TIGR02035 203 eyesdyskaveeGrkeaeadplsyfvddeksrdlflGyavaasrlkkqldkkgikvdkehplfvylpcG 271
                                               e++sdys+ave+Gr+ea++dp ++fvdde+s +lflGyavaa+rl +ql+++g++vd+ehplfvylpcG
  lcl|NCBI__GCF_000310185.1:WP_004306148.1 218 EHASDYSVAVEQGRREAASDPACHFVDDENSPQLFLGYAVAAERLAGQLQRAGVRVDAEHPLFVYLPCG 286
                                               ********************************************************************* PP

                                 TIGR02035 272 vGGgpGGvafGlkllfgddvhvffaepthspcmllGlytGlhekisvqdiGidnltaadGlavgrpsGl 340
                                               vGGgpGGvafGlk++fgd+vh++faepthspcmllG+ytGlh+++svqd+Gidn taadGlavgrpsG+
  lcl|NCBI__GCF_000310185.1:WP_004306148.1 287 VGGGPGGVAFGLKRVFGDAVHCIFAEPTHSPCMLLGVYTGLHDQVSVQDFGIDNVTAADGLAVGRPSGF 355
                                               ********************************************************************* PP

                                 TIGR02035 341 vGrllerlldGiytvddeklydllallaesedkrlepsalaglaGvvrllkeeeskreaekliakklen 409
                                               vG++++rl+dG+ytv+de l++llal + +e+ rlepsalag+ G+v +l+   ++ ++ +++ +++++
  lcl|NCBI__GCF_000310185.1:WP_004306148.1 356 VGKAMQRLIDGYYTVSDEALFRLLALAHDDEGLRLEPSALAGVPGMVCVLRD-AAYLDRIGVTPARFAR 423
                                               **************************************************98.89999*********** PP

                                 TIGR02035 410 avhlvwatGGkmvpeeemea 429
                                               a+hlvw+tGG+mvp+ e +a
  lcl|NCBI__GCF_000310185.1:WP_004306148.1 424 ATHLVWGTGGSMVPDSEFAA 443
                                               ****************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (431 nodes)
Target sequences:                          1  (456 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: 00:00:00.01
# Mc/sec: 11.84
//
[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