Alignments for a candidate for gcvT in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for gcvT in Pseudomonas fluorescens FW300-N1B4

Align Aminomethyltransferase; EC 2.1.2.10; Glycine cleavage system T protein (uncharacterized)
to candidate Pf1N1B4_2234 Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.10)

Query= curated2:Q88AS0
         (360 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2234
          Length = 277

 Score =  445 bits (1145), Expect = e-130
 Identities = 222/277 (80%), Positives = 249/277 (89%)

Query: 84  LYSAMLDEQAGVIDDMIVYLTADGYRLVVNAATGAKDLAWMQSQLGDFDVQLLARSEMAM 143
           LYSAML+E  G++DDMIVY   DGYRLVVNA+T  +DLAWMQ+ LGDFDV+L  RSE+AM
Sbjct: 1   LYSAMLNEHGGIVDDMIVYRLEDGYRLVVNASTRNQDLAWMQAHLGDFDVRLNERSELAM 60

Query: 144 LAIQGPQARNRIAQLVSSARAELIRQLKPFEGLDDGDWFIARTGYTGEDGLEIMLPADEA 203
           LAIQGP AR++IA+LV+ +R  LI+QLK FEG  DGDWFIARTGYTGEDGLEI+LPAD+A
Sbjct: 61  LAIQGPHARHKIAELVTQSRGTLIQQLKYFEGQTDGDWFIARTGYTGEDGLEIVLPADQA 120

Query: 204 QRFFNELVGAGISPIGLGARDTLRLEAGMNLYGQDIGEHVSPLASNMAWSIAWEPAERDF 263
             FFN+LVGAGISPIGLGARDTLR+EAGMNLYGQDI + VSPLASNMAWSIAWEPA R F
Sbjct: 121 PGFFNDLVGAGISPIGLGARDTLRVEAGMNLYGQDIHQEVSPLASNMAWSIAWEPATRQF 180

Query: 264 IGRQALESERAEGTAFKLVGLVLEERGVLRAHQVVRVAEIGEGEITSGSFSPTLSKSIAL 323
           IGR ALE+E+A+G   KLVGLVLEERGVLRAHQVVR+A++GEGEITSGSFSPTLSKSIAL
Sbjct: 181 IGRTALEAEQADGVQHKLVGLVLEERGVLRAHQVVRIADVGEGEITSGSFSPTLSKSIAL 240

Query: 324 ARVPMATADRAEVEIRGKWYPVRVVQPAFVRHGKTLI 360
           ARVP+ATADRAEVEIRGKWYPVRVV+P FVRHGKTLI
Sbjct: 241 ARVPVATADRAEVEIRGKWYPVRVVKPTFVRHGKTLI 277


Lambda     K      H
   0.321    0.137    0.406 

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: 383
Number of extensions: 10
Number of successful extensions: 1
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: 360
Length of database: 277
Length adjustment: 27
Effective length of query: 333
Effective length of database: 250
Effective search space:    83250
Effective search space used:    83250
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: 48 (23.1 bits)

Align candidate Pf1N1B4_2234 (Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.10))
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.9156.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
    5.9e-89  284.4   0.0    6.6e-89  284.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2234  Aminomethyltransferase (glycine 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2234  Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.3   0.0   6.6e-89   6.6e-89      83     361 ..       2     271 ..       1     272 [. 0.93

  Alignments for each domain:
  == domain 1  score: 284.3 bits;  conditional E-value: 6.6e-89
                                      TIGR00528  83 ysvllnaqGGvvDDlivykegednrfllvvnaataekDlewlkehleeevtldtlskeisllal 146
                                                    ys++ln +GG+vDD+ivy+ ++   ++lvvna+t+++Dl+w++ hl ++    + + e+++la+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2234   2 YSAMLNEHGGIVDDMIVYRLEDG--YRLVVNASTRNQDLAWMQAHLGDFDVRLNERSELAMLAI 63 
                                                    9*****************99887..*************************99************ PP

                                      TIGR00528 147 qGPkaktiledlldkaveg.lkefffvqeaelalkkaliartGytGedGfeiavanekavelwk 209
                                                    qGP+a+  + +l+ ++ +  ++++ +  e++    + +iartGytGedG ei+++ ++a  +++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2234  64 QGPHARHKIAELVTQSRGTlIQQLKYF-EGQT-DGDWFIARTGYTGEDGLEIVLPADQAPGFFN 125
                                                    ******999999999887743444444.4443.4455*************************** PP

                                      TIGR00528 210 klveaygvkPiGLgarDtLrleagmaLyGqeldeeitPleaglgwvvkkerkksdfiGravlee 273
                                                     lv a g+ PiGLgarDtLr+eagm+LyGq++++e++Pl++++ w +++e++ ++fiGr++le 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2234 126 DLVGA-GISPIGLGARDTLRVEAGMNLYGQDIHQEVSPLASNMAWSIAWEPATRQFIGRTALEA 188
                                                    *****.********************************************************** PP

                                      TIGR00528 274 qkengtekklvGlemlekgiarnelkvlltngekevGivtsGtlsPtLgknialayvdkeleki 337
                                                     +++g+++klvGl++ e+g++r +  v+ +  +  +G +tsG++sPtL k+iala+v+      
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2234 189 EQADGVQHKLVGLVLEERGVLRAHQVVRIA--DVGEGEITSGSFSPTLSKSIALARVP---VAT 247
                                                    ************************999995..5599**********************...556 PP

                                      TIGR00528 338 Gtklevevrnklvkikvvkklfvr 361
                                                     +++eve+r+k ++++vvk+ fvr
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2234 248 ADRAEVEIRGKWYPVRVVKPTFVR 271
                                                    6899******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (362 nodes)
Target sequences:                          1  (277 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: 8.97
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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