GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcvT in Pseudomonas fluorescens FW300-N2E3

Align Aminomethyltransferase (EC 2.1.2.10) (characterized)
to candidate AO353_08735 AO353_08735 glycine cleavage system protein T

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



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735 AO353_08735 glycine
           cleavage system protein T
          Length = 360

 Score =  402 bits (1033), Expect = e-117
 Identities = 205/365 (56%), Positives = 268/365 (73%), Gaps = 6/365 (1%)

Query: 1   MAQQTPLFEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGS 60
           M Q+TPL++ H   GA+MVDF GW MPLHYGSQ++EHH VR D G+FDVSHMT++D  G 
Sbjct: 1   MGQRTPLYDLHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMTVIDVSGP 60

Query: 61  RIREFLRYLLANDVAKLTVPGKALYSGMLTASGGVIDDLIVYFLSEDYFRLVVNSATREK 120
           + + +L++LLANDV +L   G+ALYS ML   GGV+DD+IVY L ED +RLVVN+ATR++
Sbjct: 61  QAKAWLQHLLANDVERLHSVGRALYSTMLNERGGVVDDMIVYRL-EDAYRLVVNAATRDQ 119

Query: 121 DLAWIAQQSESYGLEITVRDDLSLIAVQGPRAKEKAATLFTDAQRQAVEGMKPFFGVQAG 180
           D+AW+  Q  +Y +++  R +L+++A+QGP+A++K A L T ++   ++ +KPF G   G
Sbjct: 120 DMAWMQAQLGNYQVQLHERRELAMLAIQGPQARQKIAELVTQSRGTLIQQLKPFEGHCDG 179

Query: 181 DLFIATTGYTGEAGYEIALPNEQAVDFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEM 240
           D FIA TGYTGE G EIALP +QA  F+  L+ AG+ P GLGARDTLRLEAGMNLYGQ++
Sbjct: 180 DWFIARTGYTGEDGLEIALPADQAPGFFNDLVGAGISPIGLGARDTLRLEAGMNLYGQDI 239

Query: 241 DEGVSPLAANMGWTIAWEPTDRDFIGREALEMQREKGTEQ-LVGLVMTEKGVLRGGLPVR 299
            + VSPLA+NM W+IAWEP  R FIGR ALE +R  G +Q LVGLV+ E+GVLR    VR
Sbjct: 240 HQDVSPLASNMAWSIAWEPATRQFIGRAALEAERAAGVKQKLVGLVLEERGVLRAHQVVR 299

Query: 300 FSDADGNQKEGIITSGTFSPTLGYSIALARVPEGIGETAVVQIRNREMPVKVTKPVFVRN 359
            +D      EG ITSG+FSPTL  SIALARVP    + A V+IR +  PV+V KP FVR+
Sbjct: 300 IADVG----EGEITSGSFSPTLSKSIALARVPMATADRAEVEIRGKWYPVRVVKPTFVRH 355

Query: 360 GKAVV 364
           GK ++
Sbjct: 356 GKTLI 360


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: 400
Number of extensions: 10
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 AO353_08735 AO353_08735 (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.17709.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
     2e-128  414.3   0.0   2.3e-128  414.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735  AO353_08735 glycine cleavage sys


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735  AO353_08735 glycine cleavage system protein T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.1   0.0  2.3e-128  2.3e-128       2     361 ..       3     354 ..       2     355 .. 0.95

  Alignments for each domain:
  == domain 1  score: 414.1 bits;  conditional E-value: 2.3e-128
                                     TIGR00528   2 krtpLydlhtelggklvdfaGwelPvqykslieeheavrtkaGlfDvshmgkvelsGskslkfLq 66 
                                                   +rtpLydlh  lg+k+vdf+Gw +P++y+s++eeh+ vr + G+fDvshm+ +++sG+++ + Lq
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735   3 QRTPLYDLHLALGAKMVDFGGWDMPLHYGSQVEEHHQVRRDCGVFDVSHMTVIDVSGPQAKAWLQ 67 
                                                   79*************************************************************** PP

                                     TIGR00528  67 rllanDvdaLtk.GkaqysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehlee 130
                                                   +llanDv++L   G+a+ys++ln  GGvvDD+ivy+ ++   ++lvvnaat+++D++w++ +l +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735  68 HLLANDVERLHSvGRALYSTMLNERGGVVDDMIVYRLEDA--YRLVVNAATRDQDMAWMQAQLGN 130
                                                   **********877**********************98776..*********************** PP

                                     TIGR00528 131 evtldtlskeisllalqGPkaktiledlldkaveg....lkefffvqeaelalkkaliartGytG 191
                                                        + ++e+++la+qGP+a++ + +l+ ++ +     lk+f +  +++      +iartGytG
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735 131 YQVQLHERRELAMLAIQGPQARQKIAELVTQSRGTliqqLKPFEGHCDGDW-----FIARTGYTG 190
                                                   9999999**************999999999875553333888887767776.....********* PP

                                     TIGR00528 192 edGfeiavanekavelwkklveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvv 256
                                                   edG eia++ ++a  +++ lv a g+ PiGLgarDtLrleagm+LyGq+++++++Pl++++ w +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735 191 EDGLEIALPADQAPGFFNDLVGA-GISPIGLGARDTLRLEAGMNLYGQDIHQDVSPLASNMAWSI 254
                                                   ***********************.***************************************** PP

                                     TIGR00528 257 kkerkksdfiGravleeqkengtekklvGlemlekgiarnelkvlltngekevGivtsGtlsPtL 321
                                                   ++e++ ++fiGra+le  ++ g+++klvGl++ e+g++r +  v+ +  +  +G +tsG++sPtL
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735 255 AWEPATRQFIGRAALEAERAAGVKQKLVGLVLEERGVLRAHQVVRIA--DVGEGEITSGSFSPTL 317
                                                   *****************************************999995..5599************ PP

                                     TIGR00528 322 gknialayvdkelekiGtklevevrnklvkikvvkklfvr 361
                                                    k+iala+v+       +++eve+r+k ++++vvk+ fvr
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_08735 318 SKSIALARVP---MATADRAEVEIRGKWYPVRVVKPTFVR 354
                                                   **********...5567899******************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: 6.85
//
[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:

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:

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:

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, or view the source code.

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