Alignments for a candidate for sdaB in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdaB in Desulfovibrio vulgaris Hildenborough

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate 207626 DVU2147 L-serine dehydratase, putative

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



>MicrobesOnline__882:207626
          Length = 502

 Score =  648 bits (1671), Expect = 0.0
 Identities = 350/502 (69%), Positives = 381/502 (75%), Gaps = 43/502 (8%)

Query: 1   MQPLV--ATIETSLFDMFEAGPGPSSSHTIGPMKAGHDFRTLCAALPPEVLACAADIRVR 58
           MQPLV  + I  SLFD+FEAGPGPSSSHTIGPMKAG+DF   CA LP ++L  AA +RVR
Sbjct: 1   MQPLVPCSAIAISLFDLFEAGPGPSSSHTIGPMKAGYDFAQRCATLPDDILCRAAGVRVR 60

Query: 59  LFGSLSATGVGHGTTGAVLAGLLGHRPATCPPGLL-------ESLPA----LPEGERTLR 107
           LFGSLSATG GHGT  AVLAGL G  PA+CPP  L       E  PA    L +G     
Sbjct: 61  LFGSLSATGYGHGTDMAVLAGLAGQLPASCPPEYLVRPEGAGEERPATDTTLADGRYASL 120

Query: 108 LG-------PAA-----------------------LVLAEGTVRRDAVQHAYPFSNTLVM 137
           LG       P A                       L L    V  DAVQH +PFSNTLV+
Sbjct: 121 LGCEGVVPVPVAGQGQGHSASGAVVRYMMLRDGLRLPLTSACVVHDAVQHEHPFSNTLVL 180

Query: 138 ELLDAHGAVLCEREYYSVGGGFIQWKGWQPEERGRPAHPYRSMAQLRARLVETGLTIHEL 197
           ELL   GA L    YYSVGGGFIQW+GWQPEERG P HPY +M QLR  + +TGL +HE+
Sbjct: 181 ELLGDTGASLFSYTYYSVGGGFIQWEGWQPEERGAPVHPYCTMRQLRECMDDTGLALHEI 240

Query: 198 ILENEMAVTGMGRAAILDRLAAIIELMEASVRRGIEDGGPLPGTLGVHRKARVLLMRAQR 257
           ILENEMAVTG  RA+I+ RL  II LMEASV RG+   G LPGTLGV RKA  L+ RA +
Sbjct: 241 ILENEMAVTGASRASIVARLDTIIGLMEASVERGLATTGRLPGTLGVFRKASTLMARAGK 300

Query: 258 LPNEVDVFLGRLNAYAFAAAEENAAGGVIVTAPTCGAAGVMPALLYAMRHDLAIGDRAVR 317
           LP+ VD FL RLNAYAFA +EENA+GGVIVTAPTCGAAGVMPA+LYAMR+D +IGDRAVR
Sbjct: 301 LPHAVDAFLCRLNAYAFAVSEENASGGVIVTAPTCGAAGVMPAVLYAMRNDFSIGDRAVR 360

Query: 318 EGVLASAAVGFLAKHNAGIAGAEVGCQGEVGVASAMAAAMLAHARGNPVHVVENAAEIAL 377
           EGVLASAAVGFLAK NAGIAGAEVGCQGEVGVASAMAAAMLAHARGN V VVENAAEIAL
Sbjct: 361 EGVLASAAVGFLAKQNAGIAGAEVGCQGEVGVASAMAAAMLAHARGNAVRVVENAAEIAL 420

Query: 378 EHHLGLTCDPVGGYVQIPCIERNAVGAVKAYNACLLATCEDPRHHRVTLDSVIAAMAEIG 437
           EHHLGLTCDPVGGYVQIPCIERNAVGAVKAYNACL+ATCEDP+HHRVTLD+VI AMAEIG
Sbjct: 421 EHHLGLTCDPVGGYVQIPCIERNAVGAVKAYNACLVATCEDPKHHRVTLDNVIRAMAEIG 480

Query: 438 RDMNAKFKETSSGGLAVSVVEC 459
            DMNAKFKETS+GGLAVSVVEC
Sbjct: 481 HDMNAKFKETSAGGLAVSVVEC 502


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: 706
Number of extensions: 25
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 459
Length of database: 502
Length adjustment: 34
Effective length of query: 425
Effective length of database: 468
Effective search space:   198900
Effective search space used:   198900
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 207626 DVU2147 (L-serine dehydratase, putative)
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.26811.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.7e-133  430.3   3.2   1.3e-107  346.5   3.1    2.0  2  lcl|MicrobesOnline__882:207626  DVU2147 L-serine dehydratase, pu


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207626  DVU2147 L-serine dehydratase, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.0   2.1e-27   2.1e-27       1      78 [.      12      91 ..      12      97 .. 0.91
   2 !  346.5   3.1  1.3e-107  1.3e-107     103     450 .]     154     499 ..     114     499 .. 0.88

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 2.1e-27
                       TIGR00720  1 isvfdlfkiGiGPssshtvGPmkaakefveelkk..kgkleqvkrvkvdlyGslaltGkGhktdkavllGleGelpeevd 78
                                    is+fdlf+ G GPsssht+GPmka+++f+++  +   + l + + v+v l+Gsl++tG Gh+td avl Gl+G+lp +  
  lcl|MicrobesOnline__882:207626 12 ISLFDLFEAGPGPSSSHTIGPMKAGYDFAQRCATlpDDILCRAAGVRVRLFGSLSATGYGHGTDMAVLAGLAGQLPASCP 91
                                    79***************************9876522679************************************98865 PP

  == domain 2  score: 346.5 bits;  conditional E-value: 1.3e-107
                       TIGR00720 103 ikfdlekdlafkdevlplhe..nglrlkaydeegevlkektyysvGGGfivdeeelkkeeeeeeevpypfksaaellel 179
                                     +++ l++  +++d v ++h+  n+l l+++ + g+ l + tyysvGGGfi  e  +    ee+    +p+ ++++l+e 
  lcl|MicrobesOnline__882:207626 154 LRLPLTSACVVHDAVQHEHPfsNTLVLELLGDTGASLFSYTYYSVGGGFIQWEGWQP---EERGAPVHPYCTMRQLREC 229
                                     455555667778888888865599**************************8765443...334455689********** PP

                       TIGR00720 180 Ckeeglsisevvlenekalrs..eeevraklleiwkvmeecierglkaegvlpGglkvkrraaslkrklkakeetskdp 256
                                      +++gl++ e++lene+a+++   +++ a+l +i   me+++ergl++ g lpG+l v r+a++l+++  +  ++  d 
  lcl|MicrobesOnline__882:207626 230 MDDTGLALHEIILENEMAVTGasRASIVARLDTIIGLMEASVERGLATTGRLPGTLGVFRKASTLMARAGKLPHAV-D- 306
                                     ******************9874367899**************************************9998888774.3. PP

                       TIGR00720 257 lavldwvnlyalavneenaaGgrvvtaPtnGaagiiPavlayykkfveeaseekvvrflltagaiGilykenasisgae 335
                                      a l  +n ya+av+eena+Gg +vtaPt Gaag++Pavl+ +++   +  + +v + +l+++a+G l k+na i+gae
  lcl|MicrobesOnline__882:207626 307 -AFLCRLNAYAFAVSEENASGGVIVTAPTCGAAGVMPAVLYAMRN-DFSIGDRAVREGVLASAAVGFLAKQNAGIAGAE 383
                                     .346779********************************965555.456789999************************ PP

                       TIGR00720 336 vGCqgevGvacsmaaaglaellggtpeqvenaaeiamehnlGltCdPvgGlvqiPCiernaiaavkainaarlalkedg 414
                                     vGCqgevGva++maaa la++ g  ++ venaaeia+eh+lGltCdPvgG vqiPCierna++avka na+ +a  ed 
  lcl|MicrobesOnline__882:207626 384 VGCQGEVGVASAMAAAMLAHARGNAVRVVENAAEIALEHHLGLTCDPVGGYVQIPCIERNAVGAVKAYNACLVATCEDP 462
                                     **************************************************************************98887 PP

                       TIGR00720 415 .kkkvsldkvietmretGkdmkakyketskgGlavkv 450
                                      +++v+ld+vi++m e+G+dm+ak+kets+gGlav+v
  lcl|MicrobesOnline__882:207626 463 kHHRVTLDNVIRAMAEIGHDMNAKFKETSAGGLAVSV 499
                                     589*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (450 nodes)
Target sequences:                          1  (502 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: 8.45
//
[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