Alignments for a candidate for sdaB in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Sphingomonas koreensis DSMZ 15582

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate Ga0059261_0220 Ga0059261_0220 L-serine dehydratase, iron-sulfur-dependent, single chain form

Query= reanno::Cup4G11:RR42_RS20080
         (458 letters)



>FitnessBrowser__Korea:Ga0059261_0220
          Length = 463

 Score =  483 bits (1244), Expect = e-141
 Identities = 253/456 (55%), Positives = 312/456 (68%), Gaps = 9/456 (1%)

Query: 3   VSVFDLFKVGIGPSSSHTVGPMRAALMFAQGLARDGLLPQVASVRVELYGSLGATGRGHG 62
           + + DLF +GIGPSSSHTVGPMRAA  F++     G+     SV  EL+GSL  TG+GH 
Sbjct: 17  IGLADLFTIGIGPSSSHTVGPMRAAHAFSEAALDRGI---PVSVSCELFGSLALTGKGHA 73

Query: 63  TDKGVILGLLGEAPDTIDPDTIDVRLAALRASRTLSLLGTHPVPFVEKEHIVFYRREAMA 122
           TD  VILGL G  P+++DPD +   +A +++ + LSL G   VPFVE  H++F     + 
Sbjct: 74  TDTAVILGLAGHQPESVDPDAVASIVATIQSEQKLSLGGQVIVPFVEGRHLIFRSDRFLP 133

Query: 123 EHPNGMKFHAFNAGGERIREGRYLSVGGGFIITAGAANTHILEADQQLPHPFRSGRAMLE 182
            HPNGM+F A    GE   E  + S+GGG ++  G        ++  LP  F SG  +L 
Sbjct: 134 AHPNGMRFVAHYPDGEPY-ETFWYSIGGGAVVEGGCEAPR---SNVTLPMNFSSGAELLA 189

Query: 183 MAAASKKSIARLMMENECVWRSEAEVNAGLLQIWAVMQACVARGCRTDGELPGPFKVKRR 242
           +A     +IA ++  NE  WR + E +A L  + A M AC+ RG R +GELPG  KVKRR
Sbjct: 190 VAEEKGVTIADIVRANEAAWRDDTETDAFLDSLRAAMSACIERGMRGEGELPGGLKVKRR 249

Query: 243 AHDLFRNLTEHAERALADPLSVIDWVNLYAIAVNEENAAGGRVVTAPTNGAAGIIPAVLH 302
           A DL   L     R+  DP  V DWV+L+A+AVNEENAAGGRVVTAPTNGAAG+IPAVL 
Sbjct: 250 ARDLHNKLLARGPRS--DPSLVFDWVSLWALAVNEENAAGGRVVTAPTNGAAGVIPAVLR 307

Query: 303 YYDRFVPGANPQGVIDFLLTAGAIGMLYKLNASISGAEVGCQGEVGVACSMAAGALAAVM 362
           YY+ F     P G   FLLT  AIG LYK  ASIS AE+GCQGEVGVACSMAA  LAA +
Sbjct: 308 YYETFCASPTPAGARTFLLTTAAIGFLYKKRASISAAEMGCQGEVGVACSMAAAGLAAAL 367

Query: 363 GGTPEQVENAAEIGMEHNLGLTCDPVGGLVQIPCIERNAMASVKAVNAARMALRGDGMHY 422
           G T  Q+ENAAEIGMEHNLGLTCDP+GGLVQIPCIERN M ++KA+NAA +A+ GDG H 
Sbjct: 368 GATNAQIENAAEIGMEHNLGLTCDPIGGLVQIPCIERNTMGAIKAINAAYLAMHGDGSHV 427

Query: 423 VSLDSVIKTMRETGADMKTKYKETARGGLAVNIVEC 458
           VSLD+VI+TMR+TG DM++KYKETA+GGLAVN+V C
Sbjct: 428 VSLDAVIETMRQTGEDMRSKYKETAQGGLAVNVVAC 463


Lambda     K      H
   0.320    0.136    0.400 

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: 639
Number of extensions: 23
Number of successful extensions: 4
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: 463
Length adjustment: 33
Effective length of query: 425
Effective length of database: 430
Effective search space:   182750
Effective search space used:   182750
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 Ga0059261_0220 Ga0059261_0220 (L-serine dehydratase, iron-sulfur-dependent, single chain form)
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.13233.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-189  616.8   0.1   1.4e-189  616.6   0.1    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0220  Ga0059261_0220 L-serine dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0220  Ga0059261_0220 L-serine dehydratase, iron-sulfur-dependent, single chain fo
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  616.6   0.1  1.4e-189  1.4e-189       3     450 .]      19     460 ..      17     460 .. 0.97

  Alignments for each domain:
  == domain 1  score: 616.6 bits;  conditional E-value: 1.4e-189
                                 TIGR00720   3 vfdlfkiGiGPssshtvGPmkaakefveelkkkgkleqvkrvkvdlyGslaltGkGhktdkavllGleG 71 
                                               + dlf+iGiGPssshtvGPm+aa++f e+  ++g      +v+ +l+GslaltGkGh+td+av+lGl+G
  lcl|FitnessBrowser__Korea:Ga0059261_0220  19 LADLFTIGIGPSSSHTVGPMRAAHAFSEAALDRG---IPVSVSCELFGSLALTGKGHATDTAVILGLAG 84 
                                               679**************************99995...467899************************** PP

                                 TIGR00720  72 elpeevdiesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegevlke 139
                                               ++pe+vd + + ++++++++e+kl+l++q  + f + ++l+f+ d++lp h+ng+r+ a+  +ge  +e
  lcl|FitnessBrowser__Korea:Ga0059261_0220  85 HQPESVDPDAVASIVATIQSEQKLSLGGQVIVPFVEGRHLIFRsDRFLPAHPNGMRFVAHYPDGEP-YE 152
                                               *******************************************99*****************9776.78 PP

                                 TIGR00720 140 ktyysvGGGfivdeeelkkeeeeeeevpypfksaaellelCkeeglsisevvlenekalrseeevrakl 208
                                                 +ys+GGG +v+     +  ++++++p +f+s aell+  +e+g++i+++v +ne+a+r+++e++a l
  lcl|FitnessBrowser__Korea:Ga0059261_0220 153 TFWYSIGGGAVVEGGC--EAPRSNVTLPMNFSSGAELLAVAEEKGVTIADIVRANEAAWRDDTETDAFL 219
                                               99**********8654..44556779******************************************* PP

                                 TIGR00720 209 leiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeetskdplavldwvnlyalavneenaaG 277
                                                +++ +m++cierg++ eg lpGglkvkrra  l++kl a+   s dp  v+dwv+l+alavneenaaG
  lcl|FitnessBrowser__Korea:Ga0059261_0220 220 DSLRAAMSACIERGMRGEGELPGGLKVKRRARDLHNKLLARGPRS-DPSLVFDWVSLWALAVNEENAAG 287
                                               *****************************************9996.9999******************* PP

                                 TIGR00720 278 grvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqgevGvac 346
                                               grvvtaPtnGaag+iPavl+yy++f+ + +      fllt++aiG lyk++asis+ae+GCqgevGvac
  lcl|FitnessBrowser__Korea:Ga0059261_0220 288 GRVVTAPTNGAAGVIPAVLRYYETFCASPTPAGARTFLLTTAAIGFLYKKRASISAAEMGCQGEVGVAC 356
                                               ********************************************************************* PP

                                 TIGR00720 347 smaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedgk 415
                                               smaaagla++lg+t  q+enaaei+mehnlGltCdP+gGlvqiPCiern+++a+kainaa la+++dg+
  lcl|FitnessBrowser__Korea:Ga0059261_0220 357 SMAAAGLAAALGATNAQIENAAEIGMEHNLGLTCDPIGGLVQIPCIERNTMGAIKAINAAYLAMHGDGS 425
                                               ********************************************************************* PP

                                 TIGR00720 416 kkvsldkvietmretGkdmkakyketskgGlavkv 450
                                               + vsld vietmr+tG+dm++kyket++gGlav+v
  lcl|FitnessBrowser__Korea:Ga0059261_0220 426 HVVSLDAVIETMRQTGEDMRSKYKETAQGGLAVNV 460
                                               *********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (463 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.20
//
[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