Alignments for a candidate for gcvT in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Desulfovibrio vulgaris Miyazaki F

Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate 8499572 DvMF_0341 glycine cleavage system T protein (RefSeq)

Query= curated2:Q31KT1
         (372 letters)



>FitnessBrowser__Miya:8499572
          Length = 362

 Score =  257 bits (657), Expect = 3e-73
 Identities = 162/363 (44%), Positives = 209/363 (57%), Gaps = 19/363 (5%)

Query: 9   LLSSPLHSVCTSAGARFTGFAGWELPLQFQ-GLMQEHLAVRERAGLFDISHMGKFQLRGS 67
           LL +PL +   +AGA+   FAGW++P+Q+  G++ EH+  RE A LFDI HMG+F LRG 
Sbjct: 4   LLQTPLSAWHRAAGAKMAPFAGWDMPIQYPTGIIAEHVQTRESAALFDICHMGEFTLRGP 63

Query: 68  GLRAALQRLLPSDLTTLLPGQAQYSVLLNEAGGCLDDLIVYWQGIVDGVEQAFLIVNAAT 127
           G R AL R +  +L TL PG+ +Y  LLNEAGG LDDLIVY        +   L+VN A 
Sbjct: 64  GARDALSRAVSHNLETLKPGRCRYGFLLNEAGGILDDLIVY----CVAEDDYMLVVNGAC 119

Query: 128 TDSDRLWLTEHLPPAIALLDLSQDLALVAIQGPQAIAFLQPLVSCDLAELPRFSHTVTSI 187
           T+SD   L   LP  +   D+S   A + +QGP++   L+ ++     +LP F       
Sbjct: 120 TESDFAALRSRLPAVLPFEDISARTAKLDLQGPKSFDVLEAVLGESFRDLPYFGFRSVVF 179

Query: 188 AGQPAFVARTGYTGEDGCEVMLPPAAAITLWQQLTA-AGVVPCGLGARDTLRLEAAMPLY 246
            G P  V+RTGYTGE G E+ LP   A  LW  L A   V P GLGARDTLRLE  +PLY
Sbjct: 180 GGAPLLVSRTGYTGELGVELYLPWDKAEALWTALLADERVKPAGLGARDTLRLEVGLPLY 239

Query: 247 GHELDTDTNPLEAGLGWVVHLDRNPDFLGR--DRLVQAKTNGLERRLVGLELPGRNIARH 304
           GH+LD    P EAG G +  L    D++G+  DR V+         LV L +PGR  ARH
Sbjct: 240 GHDLDDTHTPAEAGYGGM--LTNPADYVGKGADREVR-------EPLVALSIPGRRSARH 290

Query: 305 GYPVAIADTTV-GIVTSGSWSPTLSKAIALAYVPPALANLGQELWVEIRGKQVPATVVKR 363
           G  VA+ D TV G+VTSGS+ P+L  A+ALA V  A A       V+    ++ AT V  
Sbjct: 291 GDVVALPDGTVAGVVTSGSFCPSLGYAVALARVAAAHAE-APTFVVKAAKVELEATRVAL 349

Query: 364 PFY 366
           PFY
Sbjct: 350 PFY 352


Lambda     K      H
   0.321    0.137    0.419 

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: 381
Number of extensions: 17
Number of successful extensions: 6
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: 372
Length of database: 362
Length adjustment: 30
Effective length of query: 342
Effective length of database: 332
Effective search space:   113544
Effective search space used:   113544
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate 8499572 DvMF_0341 (glycine cleavage system T protein (RefSeq))
to HMM TIGR00528 (gcvT: glycine cleavage system T protein (EC 2.1.2.10))

# 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/TIGR00528.hmm
# target sequence database:        /tmp/gapView.13442.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00528  [M=362]
Accession:   TIGR00528
Description: gcvT: glycine cleavage system T protein
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-86  276.9   0.0    1.3e-86  276.7   0.0    1.0  1  lcl|FitnessBrowser__Miya:8499572  DvMF_0341 glycine cleavage syste


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499572  DvMF_0341 glycine cleavage system T protein (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.7   0.0   1.3e-86   1.3e-86       2     343 ..       5     335 ..       4     354 .. 0.93

  Alignments for each domain:
  == domain 1  score: 276.7 bits;  conditional E-value: 1.3e-86
                         TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqy.kslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLt 77 
                                        +tpL   h   g+k+ +faGw +P+qy +++i eh  +r++a lfD+ hmg+++l+G+ ++++L r ++ +++ L 
  lcl|FitnessBrowser__Miya:8499572   5 LQTPLSAWHRAAGAKMAPFAGWDMPIQYpTGIIAEHVQTRESAALFDICHMGEFTLRGPGARDALSRAVSHNLETLK 81 
                                       69**************************5578********************************************* PP

                         TIGR00528  78 kGkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGPkakti 154
                                       +G+ +y  lln  GG++DDlivy  +ed  ++lvvn a++e D + l+ +l+    ++++s   + l lqGPk+ ++
  lcl|FitnessBrowser__Miya:8499572  82 PGRCRYGFLLNEAGGILDDLIVYCVAED-DYMLVVNGACTESDFAALRSRLPAVLPFEDISARTAKLDLQGPKSFDV 157
                                       ****************************.9*********************************************** PP

                         TIGR00528 155 ledlldkaveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgarDtLrle 231
                                       le +l ++  +l+ f+f     + +   l++rtGytGe G e++++ +ka  lw +l+++  vkP GLgarDtLrle
  lcl|FitnessBrowser__Miya:8499572 158 LEAVLGESFRDLPYFGFR-SVVFGGAPLLVSRTGYTGELGVELYLPWDKAEALWTALLADERVKPAGLGARDTLRLE 233
                                       *************99998.778888888************************************************* PP

                         TIGR00528 232 agmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvlltngeke 308
                                        g++LyG++ld++ tP eag g +++      d++G+ +     + ++++ lv l +  +  ar++  v l++g + 
  lcl|FitnessBrowser__Miya:8499572 234 VGLPLYGHDLDDTHTPAEAGYGGMLTNP---ADYVGKGA-----DREVREPLVALSIPGRRSARHGDVVALPDG-TV 301
                                       **********************999877...899**986.....4556677***********************.** PP

                         TIGR00528 309 vGivtsGtlsPtLgknialayvdkelekiGtklev 343
                                        G+vtsG++ P Lg+++ala+v    ++  t   v
  lcl|FitnessBrowser__Miya:8499572 302 AGVVTSGSFCPSLGYAVALARVAAAHAEAPT-FVV 335
                                       **********************976665544.334 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (362 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: 7.74
//
[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