Alignments for a candidate for gcvT in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Desulfovibrio vulgaris Hildenborough

Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate 207143 DVU1684 glycine cleavage system T protein

Query= curated2:Q31KT1
         (372 letters)



>MicrobesOnline__882:207143
          Length = 376

 Score =  256 bits (653), Expect = 9e-73
 Identities = 160/370 (43%), Positives = 213/370 (57%), Gaps = 22/370 (5%)

Query: 9   LLSSPLHSVCTSAGARFTGFAGWELPLQFQGLMQEHLAVRERAGLFDISHMGKFQLRGSG 68
           LL +PL++   + GA+   FAGW++P+Q++G++ EH   R  A LFDI HMG+F LRG G
Sbjct: 18  LLLTPLNAWHRAQGAKMAPFAGWDMPIQYEGILAEHQHTRTHAALFDICHMGEFALRGPG 77

Query: 69  LRAALQRLLPSDLTTLLPGQAQYSVLLNEAGGCLDDLIVYWQGIVDGVEQAFLIVNAATT 128
            + AL R +  +L TL PG+ +Y  LLNEAG  LDDLIVY        +   L+VN A  
Sbjct: 78  AKQALARAVTHNLETLKPGRCRYGFLLNEAGCVLDDLIVYCL----AEDDYMLVVNGACI 133

Query: 129 DSDRLWLTEHLPPAIALLDLSQDLALVAIQGPQAIAFLQPLVSCDLAELPRFSHTVTSIA 188
            SD   L E LP ++   D+S   A + +QGP++I  L+ L+     EL  F+ T T+  
Sbjct: 134 ASDFAALRERLPASLHFEDISAATAKLDLQGPKSIDALEGLLGRSFRELGYFAFTHTTFD 193

Query: 189 GQPAFVARTGYTGEDGCEVMLPPAAAITLWQQLTA-AGVVPCGLGARDTLRLEAAMPLYG 247
           G    V+RTGYTGE G E+ LP   A TLW +L   A V P GLGARDTLRLE  +PLYG
Sbjct: 194 GANLMVSRTGYTGELGYELYLPWDKAETLWTRLLENADVKPAGLGARDTLRLEVGLPLYG 253

Query: 248 HELDTDTNPLEAGLGWVVHLDRNPDFLGRDRLVQAKTNGLERRLVGLELPGRNIARHGYP 307
            +LDT   P EAG   +  L    D++G+ R        +   LV L +PGR  ARHG  
Sbjct: 254 QDLDTTHTPAEAGYEGM--LTNTVDYVGKGR-----DREVREVLVPLAIPGRRAARHGDA 306

Query: 308 VAIAD-TTVGIVTSGSWSPTLSKAIALAYVPPALAN----LGQELWVEIRGKQVPATVVK 362
           VA+ D T VG+VTSGS++P++  A+ALAYV    A     + +   VE+  K+ P     
Sbjct: 307 VALPDGTVVGVVTSGSFAPSVGHAVALAYVKKPHAEEDSFIIKAARVELEAKRAPL---- 362

Query: 363 RPFYRGSQFR 372
            PFY G   R
Sbjct: 363 -PFYAGGTAR 371


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: 386
Number of extensions: 21
Number of successful extensions: 5
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: 376
Length adjustment: 30
Effective length of query: 342
Effective length of database: 346
Effective search space:   118332
Effective search space used:   118332
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: 50 (23.9 bits)

Align candidate 207143 DVU1684 (glycine cleavage system T protein)
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.14460.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    1.1e-90  290.1   0.0    1.4e-90  289.8   0.0    1.0  1  lcl|MicrobesOnline__882:207143  DVU1684 glycine cleavage system 


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207143  DVU1684 glycine cleavage system T protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.8   0.0   1.4e-90   1.4e-90       4     337 ..      21     343 ..      18     365 .. 0.95

  Alignments for each domain:
  == domain 1  score: 289.8 bits;  conditional E-value: 1.4e-90
                       TIGR00528   4 tpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLtkGkaq 82 
                                     tpL   h  +g+k+ +faGw +P+qy+++  eh+ +rt+a lfD+ hmg++ l+G+ + ++L r ++ +++ L +G+ +
  lcl|MicrobesOnline__882:207143  21 TPLNAWHRAQGAKMAPFAGWDMPIQYEGILAEHQHTRTHAALFDICHMGEFALRGPGAKQALARAVTHNLETLKPGRCR 99 
                                     99***************************************************************************** PP

                       TIGR00528  83 ysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGPkaktiledlldk 161
                                     y  lln  G v+DDlivy  +ed  ++lvvn a++  D + l+e+l+ + +++++s   + l lqGPk+ + le ll +
  lcl|MicrobesOnline__882:207143 100 YGFLLNEAGCVLDDLIVYCLAED-DYMLVVNGACIASDFAALRERLPASLHFEDISAATAKLDLQGPKSIDALEGLLGR 177
                                     ***********************.9****************************************************** PP

                       TIGR00528 162 aveglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLgarDtLrleagmaLyGqe 240
                                     +  +l  f+f  ++ + + + +++rtGytGe G+e++++ +ka  lw +l+e+  vkP GLgarDtLrle g++LyGq+
  lcl|MicrobesOnline__882:207143 178 SFRELGYFAFT-HTTFDGANLMVSRTGYTGELGYELYLPWDKAETLWTRLLENADVKPAGLGARDTLRLEVGLPLYGQD 255
                                     **********9.889999999********************************************************** PP

                       TIGR00528 241 ldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvlltngekevGivtsGtlsP 319
                                     ld + tP eag + +++      d++G+      ++ ++++ lv l +  + +ar++  v l++g + vG+vtsG+++P
  lcl|MicrobesOnline__882:207143 256 LDTTHTPAEAGYEGMLTNT---VDYVGKG-----RDREVREVLVPLAIPGRRAARHGDAVALPDG-TVVGVVTSGSFAP 325
                                     **********999888777...8999986.....67778888***********************.************* PP

                       TIGR00528 320 tLgknialayvdkeleki 337
                                      +g+++alayv+k  ++ 
  lcl|MicrobesOnline__882:207143 326 SVGHAVALAYVKKPHAEE 343
                                     ***********9876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (376 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: 11.81
//
[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