Alignments for a candidate for nagA in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Sphingomonas koreensis DSMZ 15582

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate Ga0059261_1645 Ga0059261_1645 N-acetylglucosamine-6-phosphate deacetylase

Query= reanno::Korea:Ga0059261_1645
         (386 letters)



>FitnessBrowser__Korea:Ga0059261_1645
          Length = 386

 Score =  771 bits (1991), Expect = 0.0
 Identities = 386/386 (100%), Positives = 386/386 (100%)

Query: 1   MRIRLENGRIVTPQGVLDGTDVTVADGTIIALTPASGSGVERKIDLGGGWLLPGFIDTQV 60
           MRIRLENGRIVTPQGVLDGTDVTVADGTIIALTPASGSGVERKIDLGGGWLLPGFIDTQV
Sbjct: 1   MRIRLENGRIVTPQGVLDGTDVTVADGTIIALTPASGSGVERKIDLGGGWLLPGFIDTQV 60

Query: 61  NGGGGVLFNDQADVDAIAAIGAAHARFGTTAFLPTLISDTPDQIAAALDAVDAAIEQGVP 120
           NGGGGVLFNDQADVDAIAAIGAAHARFGTTAFLPTLISDTPDQIAAALDAVDAAIEQGVP
Sbjct: 61  NGGGGVLFNDQADVDAIAAIGAAHARFGTTAFLPTLISDTPDQIAAALDAVDAAIEQGVP 120

Query: 121 GVVGIHVEGPFINEVKRGIHEARRIRRLDADTLALFTAPRRGRVMLTLAPELCDTDDVRT 180
           GVVGIHVEGPFINEVKRGIHEARRIRRLDADTLALFTAPRRGRVMLTLAPELCDTDDVRT
Sbjct: 121 GVVGIHVEGPFINEVKRGIHEARRIRRLDADTLALFTAPRRGRVMLTLAPELCDTDDVRT 180

Query: 181 LVKHGVIVSAGHTNATYDEMMAAIGAGLTGFTHLFNAMSPLHHRNPGAVGAAFDSESWCG 240
           LVKHGVIVSAGHTNATYDEMMAAIGAGLTGFTHLFNAMSPLHHRNPGAVGAAFDSESWCG
Sbjct: 181 LVKHGVIVSAGHTNATYDEMMAAIGAGLTGFTHLFNAMSPLHHRNPGAVGAAFDSESWCG 240

Query: 241 MIVDDAHLHPAVVRLAVRAKGIERLMLVTDAMPSVGTGDTEFMLQGKRIMVRNGVCLFED 300
           MIVDDAHLHPAVVRLAVRAKGIERLMLVTDAMPSVGTGDTEFMLQGKRIMVRNGVCLFED
Sbjct: 241 MIVDDAHLHPAVVRLAVRAKGIERLMLVTDAMPSVGTGDTEFMLQGKRIMVRNGVCLFED 300

Query: 301 GTLAGTHLDMASALRNTVEVTGLSVPDVAVMASTTPAHFLSLDRYGALAPGKRADWVWLD 360
           GTLAGTHLDMASALRNTVEVTGLSVPDVAVMASTTPAHFLSLDRYGALAPGKRADWVWLD
Sbjct: 301 GTLAGTHLDMASALRNTVEVTGLSVPDVAVMASTTPAHFLSLDRYGALAPGKRADWVWLD 360

Query: 361 KDLQPRGTWIGGEPVADAEEFARAAQ 386
           KDLQPRGTWIGGEPVADAEEFARAAQ
Sbjct: 361 KDLQPRGTWIGGEPVADAEEFARAAQ 386


Lambda     K      H
   0.321    0.137    0.413 

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: 694
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: 386
Length of database: 386
Length adjustment: 30
Effective length of query: 356
Effective length of database: 356
Effective search space:   126736
Effective search space used:   126736
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: 50 (23.9 bits)

Align candidate Ga0059261_1645 Ga0059261_1645 (N-acetylglucosamine-6-phosphate deacetylase)
to HMM TIGR00221 (nagA: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25))

# 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/TIGR00221.hmm
# target sequence database:        /tmp/gapView.6062.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00221  [M=380]
Accession:   TIGR00221
Description: nagA: N-acetylglucosamine-6-phosphate deacetylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.6e-95  306.2   0.0    1.7e-95  306.1   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_1645  Ga0059261_1645 N-acetylglucosami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_1645  Ga0059261_1645 N-acetylglucosamine-6-phosphate deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.1   0.0   1.7e-95   1.7e-95       6     379 ..       4     372 ..       1     373 [. 0.95

  Alignments for each domain:
  == domain 1  score: 306.1 bits;  conditional E-value: 1.7e-95
                                 TIGR00221   6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtnda 74 
                                                l++ +i+t + vld + v ++d+ i a+++ +      ++idl g  l+pG+iD q+nG+gGv +nd+
  lcl|FitnessBrowser__Korea:Ga0059261_1645   4 RLENGRIVTPQGVLDGTDVTVADGTIIALTPASGSGV-ERKIDLGGGWLLPGFIDTQVNGGGGVLFNDQ 71 
                                               6899************************999877655.578***************************8 PP

                                 TIGR00221  75 sv.etleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGa 142
                                               +  +++  +  a a+ G+t+fLptli+   ++i  a+ ++ +++ +     ++G+h+eGPf++ +k+G+
  lcl|FitnessBrowser__Korea:Ga0059261_1645  72 ADvDAIAAIGAAHARFGTTAFLPTLISDTPDQIAAALDAVDAAIEQGVP-GVVGIHVEGPFINEVKRGI 139
                                               877****************************************999877.8****************** PP

                                 TIGR00221 143 hpkeyirepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafka 211
                                               h+   ir+ d++ l  f     + + ++tlape+   ++ +++l+++g+ivsaGhtnaty+e+ +a+ a
  lcl|FitnessBrowser__Korea:Ga0059261_1645 140 HEARRIRRLDADTLALFTAPRRGRV-MLTLAPELC-DTDDVRTLVKHGVIVSAGHTNATYDEMMAAIGA 206
                                               *************999998888876.69****665.5666799************************** PP

                                 TIGR00221 212 GitfathlynamskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaa 280
                                               G t  thl+nams+l+hR+pg++Ga+ d+ +  +++i+D  h hp+ +rla ++kg+ +l+lvtD++ +
  lcl|FitnessBrowser__Korea:Ga0059261_1645 207 GLTGFTHLFNAMSPLHHRNPGAVGAAFDS-ESWCGMIVDDAHLHPAVVRLAVRAKGIERLMLVTDAMPS 274
                                               ****************************9.889************************************ PP

                                 TIGR00221 281 agaklekfifaGkevyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgid 349
                                                g+ + +f+ +Gk +++r++ +l ++gtlaG+ l m  +++n ve +++s+ dv+ ++s  pa+ l +d
  lcl|FitnessBrowser__Korea:Ga0059261_1645 275 VGTGDTEFMLQGKRIMVRNGVCLFEDGTLAGTHLDMASALRNTVEVTGLSVPDVAVMASTTPAHFLSLD 343
                                               *******************************************************************97 PP

                                 TIGR00221 350 drlGsvakGkdanLavltkdfeviltiveg 379
                                                r G++a Gk a+ + l+kd +  +t + g
  lcl|FitnessBrowser__Korea:Ga0059261_1645 344 -RYGALAPGKRADWVWLDKDLQPRGTWIGG 372
                                               .55******************998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (386 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.77
//
[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