Alignments for a candidate for sdaB in Desulfobulbus mediterraneus DSM 13871

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Desulfobulbus mediterraneus DSM 13871

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_028585901.1 G494_RS0119770 L-serine ammonia-lyase

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



>NCBI__GCF_000429965.1:WP_028585901.1
          Length = 455

 Score =  419 bits (1078), Expect = e-122
 Identities = 230/456 (50%), Positives = 296/456 (64%), Gaps = 1/456 (0%)

Query: 4   LVATIETSLFDMFEAGPGPSSSHTIGPMKAGHDFRTLCAALPPEVLACAADIRVRLFGSL 63
           +V  I TS+FD+F+ GPGPSSSHTIGPMKA   F      LP E  A  + + V L+GSL
Sbjct: 1   MVPPISTSVFDIFKIGPGPSSSHTIGPMKAASCFLDKLQDLPAEQQAQLSSLHVHLYGSL 60

Query: 64  SATGVGHGTTGAVLAGLLGHRPATCPPGLLESLPALPEGERTLRLGPAALVLAEGTVRRD 123
           SATG+GHGT  AVLAGLLG  P +C    L  L +       ++ G  A+  +   +  D
Sbjct: 61  SATGIGHGTHKAVLAGLLGWLPESCDSDELLGLMSREGEGYQIQAGDQAIEFSREDIHFD 120

Query: 124 AVQHAYPFSNTLVMELLDAHGAVLCEREYYSVGGGFIQWKGWQPEERGRPAHPYRSMAQL 183
             +    F+NTLV       G VL E EYYS+GGGFI+ +G +   R  P H + +M +L
Sbjct: 121 GDRPGAEFANTLVFTARGPGGVVL-EAEYYSIGGGFIRSRGEEEPVRPLPVHAFSNMTEL 179

Query: 184 RARLVETGLTIHELILENEMAVTGMGRAAILDRLAAIIELMEASVRRGIEDGGPLPGTLG 243
           R  + +    + ELILENE  ++G  R  I   L  I+  M+A+V  G+   G LPG +G
Sbjct: 180 RRLVNQRQQALPELILENEEQLSGKSREEIEAGLDRILGAMQAAVDSGLAADGVLPGPIG 239

Query: 244 VHRKARVLLMRAQRLPNEVDVFLGRLNAYAFAAAEENAAGGVIVTAPTCGAAGVMPALLY 303
           + RKARVL   ++ L N  D FL  LNAY+ AA+EEN AG  +VTAPT G+AGV+P ++ 
Sbjct: 240 LQRKARVLDQHSRGLKNSHDRFLAALNAYSLAASEENGAGRKVVTAPTSGSAGVIPGVVA 299

Query: 304 AMRHDLAIGDRAVREGVLASAAVGFLAKHNAGIAGAEVGCQGEVGVASAMAAAMLAHARG 363
             R  L    R +R+G++A+AA+ F+A+HNA IAGAEVGCQGEVGVA+AMAAA LA   G
Sbjct: 300 VAREFLHYSPRQLRQGLVAAAAIAFVARHNASIAGAEVGCQGEVGVAAAMAAAFLAQGAG 359

Query: 364 NPVHVVENAAEIALEHHLGLTCDPVGGYVQIPCIERNAVGAVKAYNACLLATCEDPRHHR 423
             +H +ENAAEIALEHHLG+TCDPVGGYVQIPCIERNA+GAV AYNA LLA+  +    +
Sbjct: 360 ATIHQLENAAEIALEHHLGMTCDPVGGYVQIPCIERNAMGAVSAYNAYLLASVGEEERQK 419

Query: 424 VTLDSVIAAMAEIGRDMNAKFKETSSGGLAVSVVEC 459
           ++LD VI AM   G +M+ K+KET+ GGLAV  V C
Sbjct: 420 ISLDQVIEAMRLTGAEMSTKYKETAQGGLAVCSVHC 455


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: 528
Number of extensions: 20
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: 459
Length of database: 455
Length adjustment: 33
Effective length of query: 426
Effective length of database: 422
Effective search space:   179772
Effective search space used:   179772
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 WP_028585901.1 G494_RS0119770 (L-serine ammonia-lyase)
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.8947.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.5e-140  452.4   0.3   1.1e-139  452.1   0.3    1.0  1  lcl|NCBI__GCF_000429965.1:WP_028585901.1  G494_RS0119770 L-serine ammonia-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028585901.1  G494_RS0119770 L-serine ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.1   0.3  1.1e-139  1.1e-139       2     448 ..       8     450 ..       7     452 .. 0.92

  Alignments for each domain:
  == domain 1  score: 452.1 bits;  conditional E-value: 1.1e-139
                                 TIGR00720   2 svfdlfkiGiGPssshtvGPmkaakefveelkk..kgkleqvkrvkvdlyGslaltGkGhktdkavllG 68 
                                               svfd+fkiG GPsssht+GPmkaa+ f+++l++  +++ +q+++++v+lyGsl++tG Gh+t+kavl G
  lcl|NCBI__GCF_000429965.1:WP_028585901.1   8 SVFDIFKIGPGPSSSHTIGPMKAASCFLDKLQDlpAEQQAQLSSLHVHLYGSLSATGIGHGTHKAVLAG 76 
                                               9******************************984456788999************************** PP

                                 TIGR00720  69 leGelpeevdiesieklleeveeekklklanqkeikfdlekdlafk.devlplhenglrlkaydeegev 136
                                               l G lpe+ d ++   l+++  e  +++  + + i+f+ ++d++f+ d+   + +n+l ++a      v
  lcl|NCBI__GCF_000429965.1:WP_028585901.1  77 LLGWLPESCDSDELLGLMSREGEGYQIQA-GDQAIEFS-REDIHFDgDRPGAEFANTLVFTARGPG-GV 142
                                               ******************99888888886.7789***9.78*****99999***********9887.77 PP

                                 TIGR00720 137 lkektyysvGGGfivdeeelkkeeeeeeevpypfksaaellelCkeeglsisevvlenekalrs..eee 203
                                               + e +yys+GGGfi ++ e +     +    ++f++++el++l +++++++ e++lene+ l +   ee
  lcl|NCBI__GCF_000429965.1:WP_028585901.1 143 VLEAEYYSIGGGFIRSRGEEE---PVRPLPVHAFSNMTELRRLVNQRQQALPELILENEEQLSGksREE 208
                                               88899*********7654432...222233468**************************9986533789 PP

                                 TIGR00720 204 vraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeetskdplavldwvnlyalavne 272
                                               ++a l +i  +m+++++ gl+a+gvlpG++ ++r+a  l ++ +  ++++    + l  +n y+la +e
  lcl|NCBI__GCF_000429965.1:WP_028585901.1 209 IEAGLDRILGAMQAAVDSGLAADGVLPGPIGLQRKARVLDQHSRGLKNSH---DRFLAALNAYSLAASE 274
                                               ***************************************99877766664...4557889********* PP

                                 TIGR00720 273 enaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgaevGCqge 341
                                               en aG +vvtaPt G+ag+iP v+a +++f +  s  ++ + l++a+ai  + ++nasi+gaevGCqge
  lcl|NCBI__GCF_000429965.1:WP_028585901.1 275 ENGAGRKVVTAPTSGSAGVIPGVVAVAREFLHY-SPRQLRQGLVAAAAIAFVARHNASIAGAEVGCQGE 342
                                               *****************************9965.67789999*************************** PP

                                 TIGR00720 342 vGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlal 410
                                               vGva++maaa la+  g+t++q+enaaeia+eh+lG+tCdPvgG vqiPCierna++av a na  la 
  lcl|NCBI__GCF_000429965.1:WP_028585901.1 343 VGVAAAMAAAFLAQGAGATIHQLENAAEIALEHHLGMTCDPVGGYVQIPCIERNAMGAVSAYNAYLLAS 411
                                               ********************************************************************8 PP

                                 TIGR00720 411 kedg.kkkvsldkvietmretGkdmkakyketskgGlav 448
                                                +++ ++k+sld+vie+mr tG++m++kyket++gGlav
  lcl|NCBI__GCF_000429965.1:WP_028585901.1 412 VGEEeRQKISLDQVIEAMRLTGAEMSTKYKETAQGGLAV 450
                                               77664899******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (455 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: 9.37
//
[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