Alignments for a candidate for sdaB in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Dyella japonica UNC79MFTsu3.2

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate N515DRAFT_4369 N515DRAFT_4369 L-serine dehydratase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5557
         (458 letters)



>FitnessBrowser__Dyella79:N515DRAFT_4369
          Length = 460

 Score =  630 bits (1626), Expect = 0.0
 Identities = 319/460 (69%), Positives = 367/460 (79%), Gaps = 2/460 (0%)

Query: 1   MSLSVFDLFKIGIGPSSSHTVGPMRAAARFAEG-LRRDDLLNCTTSVKVELYGSLGATGK 59
           M++SVFDLFKIGIGPSSSHTVGPMRAAARFAE  L    +L     ++ EL+GSL  TG+
Sbjct: 1   MAVSVFDLFKIGIGPSSSHTVGPMRAAARFAERWLDEKGVLGRVARLRAELFGSLAMTGR 60

Query: 60  GHGSDKAVLLGLEGEHPDTVDTETVDARLQAIRSSGRLNLLGEHSIEFNEKLHLAMI-RK 118
           GHG+DKAVLLG EG HPD VD + +   L+ IR + RL +LG H IEF+EK  L    R+
Sbjct: 61  GHGTDKAVLLGFEGAHPDNVDPDRIPETLERIRHTKRLRVLGRHEIEFDEKRDLVFNKRQ 120

Query: 119 PLAFHPNGMIFRAFDAAGLQVRSREYYSVGGGFVVDEGAAGADRIVEDATPLTFPFKSAK 178
            L FH NGM F A+DAAG ++ +R+YYSVGGGFVV++  A  DRIV D T L +PF +  
Sbjct: 121 KLPFHTNGMRFTAYDAAGHELGTRDYYSVGGGFVVNQDEAAEDRIVADTTALPYPFSTGD 180

Query: 179 DLLGHCSTYGLSISQVMLTNESAWRPEAETRAGLLKIWQVMQDCVAAGCRNEGILPGGLK 238
            LL  C  + L+I+Q+M+ NE  WR EAETRAGLL IW+ MQDCV  G R+ G LPGGLK
Sbjct: 181 QLLALCEQHHLTIAQLMMENEKVWRSEAETRAGLLTIWKAMQDCVTRGLRSPGTLPGGLK 240

Query: 239 VKRRAAALHRQLCKNPEAALRDPLSVLDWVNLYALAVNEENAYGGRVVTAPTNGAAGIIP 298
           V RRA A+ ++L   PEAAL+DPL++LDWVNLYALAVNEENA GGRVVTAPTNGAAGI+P
Sbjct: 241 VTRRAPAMAQELRNQPEAALKDPLTILDWVNLYALAVNEENAAGGRVVTAPTNGAAGIVP 300

Query: 299 AVLHYYMRFIPGASEDGVVRFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGAL 358
           AVLHYY RF P +++DGV+ FLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAG L
Sbjct: 301 AVLHYYHRFCPKSNDDGVIEFLLTAAAIGILYKENASISGAEVGCQGEVGVACSMAAGGL 360

Query: 359 CEVLGGSVQQVENAAEIGMEHNLGLTCDPIGGLVQVPCIERNAMGSVKAINAVRMAMRGD 418
              LGG+V QVENAAEIGMEHNLGLTCDPIGGLVQ+PCIERNAMGSVKAINA RMA++ D
Sbjct: 361 TAALGGNVLQVENAAEIGMEHNLGLTCDPIGGLVQIPCIERNAMGSVKAINASRMALKSD 420

Query: 419 GHHFVSLDKVIRTMRQTGADMKSKYKETARGGLAVNIIEC 458
           G H VSLDKVI TMR TG DMK KYKET+RGGLAVN+IEC
Sbjct: 421 GKHRVSLDKVIATMRDTGRDMKDKYKETSRGGLAVNVIEC 460


Lambda     K      H
   0.320    0.136    0.401 

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: 720
Number of extensions: 26
Number of successful extensions: 3
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: 458
Length of database: 460
Length adjustment: 33
Effective length of query: 425
Effective length of database: 427
Effective search space:   181475
Effective search space used:   181475
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 N515DRAFT_4369 N515DRAFT_4369 (L-serine dehydratase)
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))

# 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/TIGR00720.hmm
# target sequence database:        /tmp/gapView.15086.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00720  [M=450]
Accession:   TIGR00720
Description: sda_mono: L-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-222  725.4   0.0   1.6e-222  725.2   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_4369  N515DRAFT_4369 L-serine dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_4369  N515DRAFT_4369 L-serine dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  725.2   0.0  1.6e-222  1.6e-222       1     450 []       3     457 ..       3     457 .. 0.98

  Alignments for each domain:
  == domain 1  score: 725.2 bits;  conditional E-value: 1.6e-222
                                    TIGR00720   1 isvfdlfkiGiGPssshtvGPmkaakefvee.lkkkgkleqvkrvkvdlyGslaltGkGhktdkav 65 
                                                  +svfdlfkiGiGPssshtvGPm+aa++f+e+ l++kg l +v+r++ +l+Gsla+tG+Gh+tdkav
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4369   3 VSVFDLFKIGIGPSSSHTVGPMRAAARFAERwLDEKGVLGRVARLRAELFGSLAMTGRGHGTDKAV 68 
                                                  69***************************975899******************************* PP

                                    TIGR00720  66 llGleGelpeevdiesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkay 130
                                                  llG+eG +p++vd ++i++ le+++++k+l++++++ei+fd+++dl+f+ +++lp+h ng+r++ay
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4369  69 LLGFEGAHPDNVDPDRIPETLERIRHTKRLRVLGRHEIEFDEKRDLVFNkRQKLPFHTNGMRFTAY 134
                                                  *************************************************999************** PP

                                    TIGR00720 131 deegevlkektyysvGGGfivdeeelkkeeeeee..evpypfksaaellelCkeeglsisevvlen 194
                                                  d +g+ l ++ yysvGGGf+v+++e+ +++  ++   +pypf++ ++ll+lC++++l+i+++++en
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4369 135 DAAGHELGTRDYYSVGGGFVVNQDEAAEDRIVADttALPYPFSTGDQLLALCEQHHLTIAQLMMEN 200
                                                  **********************999887765444349***************************** PP

                                    TIGR00720 195 ekalrseeevraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeets.kdplav 259
                                                  ek++rse+e+ra ll+iwk+m++c++rgl++ g+lpGglkv+rra++++++l+++ e+  kdpl++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4369 201 EKVWRSEAETRAGLLTIWKAMQDCVTRGLRSPGTLPGGLKVTRRAPAMAQELRNQPEAAlKDPLTI 266
                                                  ********************************************************9999****** PP

                                    TIGR00720 260 ldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGily 325
                                                  ldwvnlyalavneenaaGgrvvtaPtnGaagi+Pavl+yy++f+++++++ v++fllta+aiGily
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4369 267 LDWVNLYALAVNEENAAGGRVVTAPTNGAAGIVPAVLHYYHRFCPKSNDDGVIEFLLTAAAIGILY 332
                                                  ****************************************************************** PP

                                    TIGR00720 326 kenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPC 391
                                                  kenasisgaevGCqgevGvacsmaa+gl+++lgg++ qvenaaei+mehnlGltCdP+gGlvqiPC
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4369 333 KENASISGAEVGCQGEVGVACSMAAGGLTAALGGNVLQVENAAEIGMEHNLGLTCDPIGGLVQIPC 398
                                                  ****************************************************************** PP

                                    TIGR00720 392 iernaiaavkainaarlalkedgkkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                                  ierna+++vkaina+r+alk+dgk++vsldkvi+tmr+tG+dmk kykets+gGlav+v
  lcl|FitnessBrowser__Dyella79:N515DRAFT_4369 399 IERNAMGSVKAINASRMALKSDGKHRVSLDKVIATMRDTGRDMKDKYKETSRGGLAVNV 457
                                                  *********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (460 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: 9.68
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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