Alignments for a candidate for sdaB in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Desulfovibrio vulgaris Miyazaki F

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate 8499231 DvMF_0011 serine dehydratase alpha chain (RefSeq)

Query= reanno::Miya:8499231
         (459 letters)



>FitnessBrowser__Miya:8499231
          Length = 459

 Score =  912 bits (2357), Expect = 0.0
 Identities = 459/459 (100%), Positives = 459/459 (100%)

Query: 1   MQPLVATIETSLFDMFEAGPGPSSSHTIGPMKAGHDFRTLCAALPPEVLACAADIRVRLF 60
           MQPLVATIETSLFDMFEAGPGPSSSHTIGPMKAGHDFRTLCAALPPEVLACAADIRVRLF
Sbjct: 1   MQPLVATIETSLFDMFEAGPGPSSSHTIGPMKAGHDFRTLCAALPPEVLACAADIRVRLF 60

Query: 61  GSLSATGVGHGTTGAVLAGLLGHRPATCPPGLLESLPALPEGERTLRLGPAALVLAEGTV 120
           GSLSATGVGHGTTGAVLAGLLGHRPATCPPGLLESLPALPEGERTLRLGPAALVLAEGTV
Sbjct: 61  GSLSATGVGHGTTGAVLAGLLGHRPATCPPGLLESLPALPEGERTLRLGPAALVLAEGTV 120

Query: 121 RRDAVQHAYPFSNTLVMELLDAHGAVLCEREYYSVGGGFIQWKGWQPEERGRPAHPYRSM 180
           RRDAVQHAYPFSNTLVMELLDAHGAVLCEREYYSVGGGFIQWKGWQPEERGRPAHPYRSM
Sbjct: 121 RRDAVQHAYPFSNTLVMELLDAHGAVLCEREYYSVGGGFIQWKGWQPEERGRPAHPYRSM 180

Query: 181 AQLRARLVETGLTIHELILENEMAVTGMGRAAILDRLAAIIELMEASVRRGIEDGGPLPG 240
           AQLRARLVETGLTIHELILENEMAVTGMGRAAILDRLAAIIELMEASVRRGIEDGGPLPG
Sbjct: 181 AQLRARLVETGLTIHELILENEMAVTGMGRAAILDRLAAIIELMEASVRRGIEDGGPLPG 240

Query: 241 TLGVHRKARVLLMRAQRLPNEVDVFLGRLNAYAFAAAEENAAGGVIVTAPTCGAAGVMPA 300
           TLGVHRKARVLLMRAQRLPNEVDVFLGRLNAYAFAAAEENAAGGVIVTAPTCGAAGVMPA
Sbjct: 241 TLGVHRKARVLLMRAQRLPNEVDVFLGRLNAYAFAAAEENAAGGVIVTAPTCGAAGVMPA 300

Query: 301 LLYAMRHDLAIGDRAVREGVLASAAVGFLAKHNAGIAGAEVGCQGEVGVASAMAAAMLAH 360
           LLYAMRHDLAIGDRAVREGVLASAAVGFLAKHNAGIAGAEVGCQGEVGVASAMAAAMLAH
Sbjct: 301 LLYAMRHDLAIGDRAVREGVLASAAVGFLAKHNAGIAGAEVGCQGEVGVASAMAAAMLAH 360

Query: 361 ARGNPVHVVENAAEIALEHHLGLTCDPVGGYVQIPCIERNAVGAVKAYNACLLATCEDPR 420
           ARGNPVHVVENAAEIALEHHLGLTCDPVGGYVQIPCIERNAVGAVKAYNACLLATCEDPR
Sbjct: 361 ARGNPVHVVENAAEIALEHHLGLTCDPVGGYVQIPCIERNAVGAVKAYNACLLATCEDPR 420

Query: 421 HHRVTLDSVIAAMAEIGRDMNAKFKETSSGGLAVSVVEC 459
           HHRVTLDSVIAAMAEIGRDMNAKFKETSSGGLAVSVVEC
Sbjct: 421 HHRVTLDSVIAAMAEIGRDMNAKFKETSSGGLAVSVVEC 459


Lambda     K      H
   0.321    0.136    0.406 

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: 804
Number of extensions: 23
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: 459
Length of database: 459
Length adjustment: 33
Effective length of query: 426
Effective length of database: 426
Effective search space:   181476
Effective search space used:   181476
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 8499231 DvMF_0011 (serine dehydratase alpha chain (RefSeq))
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.21986.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.8e-135  437.6   0.1   3.3e-135  437.4   0.1    1.0  1  lcl|FitnessBrowser__Miya:8499231  DvMF_0011 serine dehydratase alp


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499231  DvMF_0011 serine dehydratase alpha chain (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.4   0.1  3.3e-135  3.3e-135       2     450 .]      11     456 ..      10     456 .. 0.91

  Alignments for each domain:
  == domain 1  score: 437.4 bits;  conditional E-value: 3.3e-135
                         TIGR00720   2 svfdlfkiGiGPssshtvGPmkaakefveelkk..kgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpee 76 
                                       s+fd+f+ G GPsssht+GPmka+++f +       + l+  + ++v l+Gsl++tG Gh+t  avl Gl G+ p +
  lcl|FitnessBrowser__Miya:8499231  11 SLFDMFEAGPGPSSSHTIGPMKAGHDFRTLCAAlpPEVLACAADIRVRLFGSLSATGVGHGTTGAVLAGLLGHRPAT 87 
                                       89************************966544311469*************************************** PP

                         TIGR00720  77 vdiesieklleeveeekklklanqkeikfdlekdlafkdevlplhenglrlkaydeegevlkektyysvGGGfivde 153
                                             e+l +  e e++l+l+    +  + +   +  +++     n+l ++++d +g+vl+e++yysvGGGfi  +
  lcl|FitnessBrowser__Miya:8499231  88 CPPGLLESLPALPEGERTLRLGPAALVLAEGTVRRDAVQHAY-PFSNTLVMELLDAHGAVLCEREYYSVGGGFIQWK 163
                                       *********999999******877666544333333333333.468****************************655 PP

                         TIGR00720 154 eelkkeeeeeeevpypfksaaellelCkeeglsisevvlenekalrs..eeevraklleiwkvmeecierglkaegv 228
                                            + ee+ + ++p++s+a+l++   e+gl+i e++lene+a+++   +++ ++l++i + me++++rg++  g 
  lcl|FitnessBrowser__Miya:8499231 164 G---WQPEERGRPAHPYRSMAQLRARLVETGLTIHELILENEMAVTGmgRAAILDRLAAIIELMEASVRRGIEDGGP 237
                                       4...44555667899*****************************987558999************************ PP

                         TIGR00720 229 lpGglkvkrraaslkrklkakeetskdplavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfvee 305
                                       lpG+l v+r+a  l  + ++  ++       l  +n ya+a +eenaaGg +vtaPt Gaag++Pa+l y+ +    
  lcl|FitnessBrowser__Miya:8499231 238 LPGTLGVHRKARVLLMRAQRLPNE---VDVFLGRLNAYAFAAAEENAAGGVIVTAPTCGAAGVMPALL-YAMRHDLA 310
                                       *************98877666655...3456899********************************77.77778888 PP

                         TIGR00720 306 aseekvvrflltagaiGilykenasisgaevGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdP 382
                                         + +v + +l+++a+G l k+na i+gaevGCqgevGva++maaa la++ g  ++ venaaeia+eh+lGltCdP
  lcl|FitnessBrowser__Miya:8499231 311 IGDRAVREGVLASAAVGFLAKHNAGIAGAEVGCQGEVGVASAMAAAMLAHARGNPVHVVENAAEIALEHHLGLTCDP 387
                                       9999************************************************************************* PP

                         TIGR00720 383 vgGlvqiPCiernaiaavkainaarlalkedg.kkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                       vgG vqiPCierna++avka na+ la  ed  +++v+ld+vi++m e+G+dm+ak+kets gGlav+v
  lcl|FitnessBrowser__Miya:8499231 388 VGGYVQIPCIERNAVGAVKAYNACLLATCEDPrHHRVTLDSVIAAMAEIGRDMNAKFKETSSGGLAVSV 456
                                       ***************************99887699*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (459 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: 7.49
//
[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