Alignments for a candidate for gcvT in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Pseudomonas benzenivorans DSM 8628

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate WP_090443902.1 BLS63_RS11170 glycine cleavage system protein T

Query= reanno::Koxy:BWI76_RS23880
         (364 letters)



>NCBI__GCF_900100495.1:WP_090443902.1
          Length = 365

 Score =  416 bits (1068), Expect = e-121
 Identities = 212/369 (57%), Positives = 269/369 (72%), Gaps = 9/369 (2%)

Query: 1   MAQQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGS 60
           M Q+TPL++ H   GA+MVDF GW MPLHYGSQ++EHH VR D G+FDVSHM ++D  GS
Sbjct: 1   MGQRTPLYDLHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMCVIDVAGS 60

Query: 61  RIREFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLS----EDYFRLVVNSA 116
           + + +L++LLANDV  L +PGKALYSGML   GGV+DDLIVY       E  +RLVVN+A
Sbjct: 61  QAKAYLQHLLANDVEHLQLPGKALYSGMLNQQGGVVDDLIVYLTGCSAQEPGYRLVVNAA 120

Query: 117 TREKDLAWIAQQSESYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFG 176
           TR KDLAW+ +QS  + +E+  R +L+++A+QGP+A+ K A L T A+   +  +KPF G
Sbjct: 121 TRAKDLAWMREQSADFAVELHERSELAMLAIQGPQARAKTAELVTQARAALIHELKPFQG 180

Query: 177 VQAGDLFIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLY 236
           +  GD FIA TGYTGE G EI LP +QAV F   L+ AG+ P GLGARDTLRLEAGMNLY
Sbjct: 181 LAEGDWFIARTGYTGEDGLEIMLPADQAVAFLNDLVGAGISPIGLGARDTLRLEAGMNLY 240

Query: 237 GQEMDEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGTE-QLVGLVMTEKGVLRGG 295
           GQ+MD+ VSPLAANM W+IAW P  R F+GR ALE Q+  G++ +LVGLV+ E+GVLR  
Sbjct: 241 GQDMDDSVSPLAANMAWSIAWAPASRRFVGRAALEAQQAAGSQPKLVGLVLEERGVLRAH 300

Query: 296 LPVRFSDADGNQKEGIITSGTFSPTLGYSIALARVPEGIGETAVVQIRNREMPVKVTKPV 355
             VR +       +G ITSG+FSP+LG SIALARVP   GE A V+IR +  PV+V KP 
Sbjct: 301 QVVRVAGVG----DGEITSGSFSPSLGKSIALARVPAQTGERAEVEIRGKWYPVRVVKPS 356

Query: 356 FVRNGKAVV 364
           FVR+GKA++
Sbjct: 357 FVRHGKALI 365


Lambda     K      H
   0.320    0.137    0.407 

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: 417
Number of extensions: 13
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: 365
Length adjustment: 29
Effective length of query: 335
Effective length of database: 336
Effective search space:   112560
Effective search space used:   112560
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 WP_090443902.1 BLS63_RS11170 (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.23040.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-131  424.6   0.0   1.6e-131  424.4   0.0    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090443902.1  BLS63_RS11170 glycine cleavage s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090443902.1  BLS63_RS11170 glycine cleavage system protein T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.4   0.0  1.6e-131  1.6e-131       2     361 ..       3     359 ..       2     360 .. 0.94

  Alignments for each domain:
  == domain 1  score: 424.4 bits;  conditional E-value: 1.6e-131
                                 TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrlla 70 
                                               +rtpLydlh  lg+k+vdf+Gw +P++y+s++eeh+ vr + G+fDvshm  ++++Gs++ ++Lq+lla
  lcl|NCBI__GCF_900100495.1:WP_090443902.1   3 QRTPLYDLHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMCVIDVAGSQAKAYLQHLLA 71 
                                               79******************************************************************* PP

                                 TIGR00528  71 nDvdaLtk.GkaqysvllnaqGGvvDDlivykeged.n..rfllvvnaataekDlewlkehleeevtld 135
                                               nDv++L   Gka+ys++ln qGGvvDDlivy +g   +   ++lvvnaat+ kDl+w++e+ ++++ + 
  lcl|NCBI__GCF_900100495.1:WP_090443902.1  72 NDVEHLQLpGKALYSGMLNQQGGVVDDLIVYLTGCSaQepGYRLVVNAATRAKDLAWMREQSADFAVEL 140
                                               ******977**********************9875532248**************************** PP

                                 TIGR00528 136 tlskeisllalqGP....kaktiledlldkaveglkefffvqeaelalkkaliartGytGedGfeiava 200
                                               + + e+++la+qGP    k ++++ ++  + +++lk+f ++ e++      +iartGytGedG ei+++
  lcl|NCBI__GCF_900100495.1:WP_090443902.1 141 HERSELAMLAIQGPqaraKTAELVTQARAALIHELKPFQGLAEGDW-----FIARTGYTGEDGLEIMLP 204
                                               **************443333445555555667789*****999999.....****************** PP

                                 TIGR00528 201 nekavelwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGra 269
                                                ++av + + lv a g+ PiGLgarDtLrleagm+LyGq++d++++Pl+a++ w +++ ++ + f+Gra
  lcl|NCBI__GCF_900100495.1:WP_090443902.1 205 ADQAVAFLNDLVGA-GISPIGLGARDTLRLEAGMNLYGQDMDDSVSPLAANMAWSIAWAPASRRFVGRA 272
                                               **************.****************************************************** PP

                                 TIGR00528 270 vleeqkengtekklvGlemlekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkelekiG 338
                                               +le q++ g++ klvGl++ e+g++r +  v+   g    G +tsG++sP Lgk+iala+v+   ++ G
  lcl|NCBI__GCF_900100495.1:WP_090443902.1 273 ALEAQQAAGSQPKLVGLVLEERGVLRAHQVVRV-AG-VGDGEITSGSFSPSLGKSIALARVP---AQTG 336
                                               ***************************999999.55.789**********************...999* PP

                                 TIGR00528 339 tklevevrnklvkikvvkklfvr 361
                                               +++eve+r+k ++++vvk+ fvr
  lcl|NCBI__GCF_900100495.1:WP_090443902.1 337 ERAEVEIRGKWYPVRVVKPSFVR 359
                                               *********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (365 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.72
//
[ok]

This GapMind analysis is from Sep 24 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