Alignments for a candidate for gcvT in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Pseudomonas stutzeri RCH2

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate GFF180 Psest_0181 glycine cleavage system T protein

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__psRCH2:GFF180
          Length = 360

 Score =  425 bits (1092), Expect = e-123
 Identities = 215/364 (59%), Positives = 270/364 (74%), Gaps = 6/364 (1%)

Query: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
           M Q+TPLY+QH   GA+MVDF GW MPLHYGSQ++EHH VR D G+FDVSHMT+VD+ G 
Sbjct: 1   MGQRTPLYDQHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMTVVDVAGE 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
           +   +L++LLANDV +L  +G+ALY+ MLN  GGVIDDLIVY  +E  +RLVVN++TREK
Sbjct: 61  QATAYLQHLLANDVTRLKGTGRALYTAMLNERGGVIDDLIVY-LSEWGYRLVVNASTREK 119

Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180
           DL+W+ Q A  F +E+  R +L+M+A+QGP+A+ + A L + A+   ++ +KPF G+  G
Sbjct: 120 DLAWMQQQAAGFAVEVKERPELAMLAIQGPHARTRTAELVSQARATLIQELKPFQGLAEG 179

Query: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240
           D FI  TGYTGE G EI LP E+A DF   LV AG+ P GLGARDTLRLEAG+NLYGQ+M
Sbjct: 180 DWFIGRTGYTGEDGLEIILPAEQAPDFLSELVGAGIPPIGLGARDTLRLEAGLNLYGQDM 239

Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHG-TEKLVGLVMTEKGVLRNELPVR 299
            E +SPLAANMGWT+AWEP +RDF+GR ALE QR  G   KLVGLV+ E+GVLR    VR
Sbjct: 240 TEDVSPLAANMGWTVAWEPTERDFVGRAALEQQRAQGDLPKLVGLVLEERGVLRAHQVVR 299

Query: 300 FTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRN 359
                    +G ITSG+FSPTLG SIALARVP G GE A V+IR +  PV+V +P FVR+
Sbjct: 300 VNGV----GDGEITSGSFSPTLGKSIALARVPAGTGERAEVEIRGKWYPVRVVQPTFVRH 355

Query: 360 GKAV 363
           GK +
Sbjct: 356 GKVL 359


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: 413
Number of extensions: 9
Number of successful extensions: 4
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: 360
Length adjustment: 29
Effective length of query: 335
Effective length of database: 331
Effective search space:   110885
Effective search space used:   110885
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 GFF180 Psest_0181 (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.31910.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   3.2e-132  426.8   0.0   3.6e-132  426.6   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF180  Psest_0181 glycine cleavage syst


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF180  Psest_0181 glycine cleavage system T protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.6   0.0  3.6e-132  3.6e-132       2     361 ..       3     354 ..       2     355 .. 0.96

  Alignments for each domain:
  == domain 1  score: 426.6 bits;  conditional E-value: 3.6e-132
                          TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaLt 77 
                                        +rtpLyd+h  lg+k+vdf+Gw +P++y+s++eeh+ vr + G+fDvshm+ v+++G+++ ++Lq+llanDv +L 
  lcl|FitnessBrowser__psRCH2:GFF180   3 QRTPLYDQHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMTVVDVAGEQATAYLQHLLANDVTRLK 78 
                                        79*************************************************************************9 PP

                          TIGR00528  78 k.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGPkak 152
                                          G+a+y+++ln  GGv+DDlivy ++    ++lvvna+t+ekDl+w+++++++++ + + + e+++la+qGP+a+
  lcl|FitnessBrowser__psRCH2:GFF180  79 GtGRALYTAMLNERGGVIDDLIVYLSEWG--YRLVVNASTREKDLAWMQQQAAGFAVEVKERPELAMLAIQGPHAR 152
                                        77**********************98877..******************************************999 PP

                          TIGR00528 153 tiledlldka....veglkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiGLga 224
                                        t   +l+++a    +++lk+f ++ e++      +i rtGytGedG ei+++ e+a ++  +lv a g+ PiGLga
  lcl|FitnessBrowser__psRCH2:GFF180 153 TRTAELVSQAratlIQELKPFQGLAEGDW-----FIGRTGYTGEDGLEIILPAEQAPDFLSELVGA-GIPPIGLGA 222
                                        88888877763333677999999999998.....********************************.********* PP

                          TIGR00528 225 rDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarnelkv 300
                                        rDtLrleag++LyGq+++e+++Pl+a++gw+v++e++++df+Gra+le+q+++g   klvGl++ e+g++r +  v
  lcl|FitnessBrowser__psRCH2:GFF180 223 RDTLRLEAGLNLYGQDMTEDVSPLAANMGWTVAWEPTERDFVGRAALEQQRAQGDLPKLVGLVLEERGVLRAHQVV 298
                                        ***********************************************************************99999 PP

                          TIGR00528 301 lltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                        +  ng    G +tsG++sPtLgk+iala+v+   ++ G+++eve+r+k ++++vv++ fvr
  lcl|FitnessBrowser__psRCH2:GFF180 299 RV-NG-VGDGEITSGSFSPTLGKSIALARVP---AGTGERAEVEIRGKWYPVRVVQPTFVR 354
                                        88.99.899**********************...899**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (360 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: 11.12
//
[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