Alignments for a candidate for gcvT in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Burkholderia phytofirmans PsJN

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate BPHYT_RS19320 BPHYT_RS19320 glycine cleavage system protein T

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__BFirm:BPHYT_RS19320
          Length = 372

 Score =  351 bits (901), Expect = e-101
 Identities = 199/376 (52%), Positives = 245/376 (65%), Gaps = 23/376 (6%)

Query: 3   QQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGSRT 62
           + TPL   H    ARMVDF GW MP++YGSQIDEH AVRTDAGMFDVSHM +VD  G R 
Sbjct: 5   KHTPLNATHRALNARMVDFGGWDMPVNYGSQIDEHRAVRTDAGMFDVSHMCVVDFTGERV 64

Query: 63  REFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREKDL 122
           R F  Y LAN+VAKL   G+ALYS +LN  GGVIDDLIVYYF ED FR+VVN+ T +KD+
Sbjct: 65  RAFFEYALANNVAKLQTPGRALYSCLLNPDGGVIDDLIVYYFGEDHFRVVVNAGTADKDI 124

Query: 123 SWITQ-HAE-PFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQA- 179
           +W  Q +AE  FG+ IT R D +++AVQGPNA+ K       A R A E +KPF   +  
Sbjct: 125 AWFGQLNAEGSFGLTITPRRDYAIVAVQGPNAREKVWQTV-PAARAATEALKPFNAARIE 183

Query: 180 ----GDLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNL 235
               G+L +A TGYTGE G+EI +P +     W AL   GV+P GLGARDTLRLEAGMNL
Sbjct: 184 DTPFGELTVARTGYTGEDGFEIIVPADHVEALWNALQAQGVRPAGLGARDTLRLEAGMNL 243

Query: 236 YGQEMDETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTEKLVGLVMTEK-----G 290
           YGQ+MD+ +SPL A + WT+    + RDF+G+  LE          VGL++ ++     G
Sbjct: 244 YGQDMDDNVSPLDAGLAWTVDL-TSPRDFVGKGKLEADGSQAA--FVGLILLKENGKAAG 300

Query: 291 VLRNELPVRFTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGI--GETAIVQIRNREMP 348
           VLR    V          EG ITSGTFSPT+  SIA ARVP+G+  G+T  VQIR++ +P
Sbjct: 301 VLRAHQKVVTPHG-----EGEITSGTFSPTMQESIAFARVPKGVQPGDTVHVQIRDKNVP 355

Query: 349 VKVTKPVFVRNGKAVA 364
             V K  FVRNGK +A
Sbjct: 356 ASVVKLPFVRNGKVLA 371


Lambda     K      H
   0.320    0.136    0.402 

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: 425
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: 364
Length of database: 372
Length adjustment: 30
Effective length of query: 334
Effective length of database: 342
Effective search space:   114228
Effective search space used:   114228
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: 49 (23.5 bits)

Align candidate BPHYT_RS19320 BPHYT_RS19320 (glycine cleavage system protein T)
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.20564.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   3.3e-121  390.5   0.0   3.7e-121  390.4   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS19320  BPHYT_RS19320 glycine cleavage s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS19320  BPHYT_RS19320 glycine cleavage system protein T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.4   0.0  3.7e-121  3.7e-121       1     362 []       4     366 ..       4     366 .. 0.92

  Alignments for each domain:
  == domain 1  score: 390.4 bits;  conditional E-value: 3.7e-121
                                TIGR00528   1 lkrtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrlla 70 
                                              lk+tpL   h  l +++vdf+Gw +Pv+y+s+i+eh+avrt+aG+fDvshm  v+ +G+++++f+++ la
  lcl|FitnessBrowser__BFirm:BPHYT_RS19320   4 LKHTPLNATHRALNARMVDFGGWDMPVNYGSQIDEHRAVRTDAGMFDVSHMCVVDFTGERVRAFFEYALA 73 
                                              689******************************************************************* PP

                                TIGR00528  71 nDvdaLtk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeev..tldtl 137
                                              n+v++L + G+a+ys lln++GGv+DDlivy++ged +f++vvna+ta+kD +w+ +  +e++    +t 
  lcl|FitnessBrowser__BFirm:BPHYT_RS19320  74 NNVAKLQTpGRALYSCLLNPDGGVIDDLIVYYFGED-HFRVVVNAGTADKDIAWFGQLNAEGSfgLTITP 142
                                              ******655***************************.******************997666541156788 PP

                                TIGR00528 138 skeisllalqGPkakt.ile..dlldkaveglkefffvqeaelalkkaliartGytGedGfeiavaneka 204
                                              +++ +++a+qGP+a++ + +  ++ ++a e+lk+f     ++    +  +artGytGedGfei+v+ ++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS19320 143 RRDYAIVAVQGPNAREkVWQtvPAARAATEALKPFNAARIEDTPFGELTVARTGYTGEDGFEIIVPADHV 212
                                              9999********9965276633567888899******99999999999********************** PP

                                TIGR00528 205 velwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeq 274
                                                lw++l ++ gv+P GLgarDtLrleagm+LyGq++d++++Pl+agl w+v +  + +df+G+ +le  
  lcl|FitnessBrowser__BFirm:BPHYT_RS19320 213 EALWNALQAQ-GVRPAGLGARDTLRLEAGMNLYGQDMDDNVSPLDAGLAWTVDLT-SPRDFVGKGKLEAD 280
                                              *******999.********************************************.9**********865 PP

                                TIGR00528 275 kengtekklvGlemle...k..giarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiGt 339
                                                 g++   vGl +l+   k  g++r + kv++++g   +G +tsGt+sPt++ +ia a+v+k++ + G+
  lcl|FitnessBrowser__BFirm:BPHYT_RS19320 281 ---GSQAAFVGLILLKengKaaGVLRAHQKVVTPHG---EGEITSGTFSPTMQESIAFARVPKGV-QPGD 343
                                              ...666667777777522233359*********999...9**********************887.57** PP

                                TIGR00528 340 klevevrnklvkikvvkklfvrs 362
                                              +++v++r+k v++ vvk +fvr+
  lcl|FitnessBrowser__BFirm:BPHYT_RS19320 344 TVHVQIRDKNVPASVVKLPFVRN 366
                                              *********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (372 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: 11.70
//
[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