Alignments for a candidate for gcvT in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Pseudomonas simiae WCS417

Align aminomethyltransferase; EC 2.1.2.10 (characterized)
to candidate GFF5324 PS417_27255 glycine cleavage system protein T

Query= CharProtDB::CH_000563
         (364 letters)



>FitnessBrowser__WCS417:GFF5324
          Length = 360

 Score =  402 bits (1032), Expect = e-116
 Identities = 203/364 (55%), Positives = 265/364 (72%), Gaps = 6/364 (1%)

Query: 1   MAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
           M Q+TPLY+ H   GA+MVDF GW MPLHYGSQ++EHH VR D G+FDVSHMT++D+ G 
Sbjct: 1   MGQRTPLYDLHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMTVIDVTGP 60

Query: 61  RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
           + +E+L+YLLANDV +L   G+ALYS MLN  GGV+DD+IVY  TE  +RLVVN++TR++
Sbjct: 61  QAKEWLQYLLANDVERLHDCGRALYSAMLNEKGGVVDDMIVYR-TESAYRLVVNASTRDQ 119

Query: 121 DLSWITQHAEPFGIEITVRDDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAG 180
           D++W+      + +++  R +L+M+A+QGP+A+ K A L   ++   +  +KPF G   G
Sbjct: 120 DMTWMHAQLGNYQVQLHERPELAMLAIQGPHARQKIAELVTQSRSTLIHQLKPFEGQADG 179

Query: 181 DLFIATTGYTGEAGYEIALPNEKAADFWRALVEAGVKPCGLGARDTLRLEAGMNLYGQEM 240
           D FIA TGYTGE G EI LP ++A  F+  LV AG+ P GLGARDTLRLEAGMNLYGQ++
Sbjct: 180 DWFIARTGYTGEDGLEIVLPADQAPGFFNDLVGAGISPIGLGARDTLRLEAGMNLYGQDI 239

Query: 241 DETISPLAANMGWTIAWEPADRDFIGREALEVQREHGTE-KLVGLVMTEKGVLRNELPVR 299
            + ISPLA+NM W+IAWEPA+R+FIGR ALE ++  G + KLVGLV+ E+GVLR    VR
Sbjct: 240 HQDISPLASNMAWSIAWEPAERNFIGRAALEAEKATGVQFKLVGLVLEERGVLRAHQVVR 299

Query: 300 FTDAQGNQHEGIITSGTFSPTLGYSIALARVPEGIGETAIVQIRNREMPVKVTKPVFVRN 359
                 N  EG ITSG+FSPTL  SIALARVP    + A V+IR +  PV+V KP FVR+
Sbjct: 300 I----ANIGEGEITSGSFSPTLSKSIALARVPTATADRAEVEIRGKWYPVRVVKPTFVRH 355

Query: 360 GKAV 363
           GK +
Sbjct: 356 GKTL 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: 406
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: 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 GFF5324 PS417_27255 (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.17356.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   8.9e-129  415.4   0.0     1e-128  415.3   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF5324  PS417_27255 glycine cleavage sys


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF5324  PS417_27255 glycine cleavage system protein T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.3   0.0    1e-128    1e-128       2     361 ..       3     354 ..       2     355 .. 0.95

  Alignments for each domain:
  == domain 1  score: 415.3 bits;  conditional E-value: 1e-128
                           TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLqrllanDvdaL 76 
                                         +rtpLydlh  lg+k+vdf+Gw +P++y+s++eeh+ vr + G+fDvshm+ ++++G+++ + Lq+llanDv++L
  lcl|FitnessBrowser__WCS417:GFF5324   3 QRTPLYDLHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMTVIDVTGPQAKEWLQYLLANDVERL 77 
                                         79************************************************************************* PP

                           TIGR00528  77 tk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllalqGPk 150
                                            G+a+ys++ln +GGvvDD+ivy+++    ++lvvna+t+++D+ w++ +l +     + + e+++la+qGP+
  lcl|FitnessBrowser__WCS417:GFF5324  78 HDcGRALYSAMLNEKGGVVDDMIVYRTESA--YRLVVNASTRDQDMTWMHAQLGNYQVQLHERPELAMLAIQGPH 150
                                         999**********************97766..***********************99999999***********9 PP

                           TIGR00528 151 aktiledlldkaveg....lkefffvqeaelalkkaliartGytGedGfeiavanekavelwkklveaygvkPiG 221
                                         a++ + +l+ ++ +     lk+f +  +++      +iartGytGedG ei+++ ++a  +++ lv a g+ PiG
  lcl|FitnessBrowser__WCS417:GFF5324 151 ARQKIAELVTQSRSTlihqLKPFEGQADGDW-----FIARTGYTGEDGLEIVLPADQAPGFFNDLVGA-GISPIG 219
                                         9988888888775554334899988877777.....********************************.****** PP

                           TIGR00528 222 LgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravleeqkengtekklvGlemlekgiarn 296
                                         LgarDtLrleagm+LyGq+++++i+Pl++++ w +++e+++++fiGra+le  k+ g++ klvGl++ e+g++r 
  lcl|FitnessBrowser__WCS417:GFF5324 220 LGARDTLRLEAGMNLYGQDIHQDISPLASNMAWSIAWEPAERNFIGRAALEAEKATGVQFKLVGLVLEERGVLRA 294
                                         *************************************************************************** PP

                           TIGR00528 297 elkvlltngekevGivtsGtlsPtLgknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                         +  v+   ++  +G +tsG++sPtL k+iala+v++      +++eve+r+k ++++vvk+ fvr
  lcl|FitnessBrowser__WCS417:GFF5324 295 HQVVRI--ANIGEGEITSGSFSPTLSKSIALARVPTA---TADRAEVEIRGKWYPVRVVKPTFVR 354
                                         *99999..5669***********************55...567899*****************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.39
//
[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