GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Pseudomonas fluorescens FW300-N2E3

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate AO353_04450 AO353_04450 N-acetylglucosamine-6-phosphate deacetylase

Query= reanno::pseudo3_N2E3:AO353_04450
         (368 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04450
          Length = 368

 Score =  744 bits (1922), Expect = 0.0
 Identities = 368/368 (100%), Positives = 368/368 (100%)

Query: 1   MSEDNILTAQGWIRGRLIHEHGKIVRIEGQPCDPADNDLPYLLPGFIDLHVHGGGGKDIM 60
           MSEDNILTAQGWIRGRLIHEHGKIVRIEGQPCDPADNDLPYLLPGFIDLHVHGGGGKDIM
Sbjct: 1   MSEDNILTAQGWIRGRLIHEHGKIVRIEGQPCDPADNDLPYLLPGFIDLHVHGGGGKDIM 60

Query: 61  EGTPAFDTITKTHVRFGTTSLLATTMTAPPEEISRVLAEVGEFCEQRPKGCARVLGVHLE 120
           EGTPAFDTITKTHVRFGTTSLLATTMTAPPEEISRVLAEVGEFCEQRPKGCARVLGVHLE
Sbjct: 61  EGTPAFDTITKTHVRFGTTSLLATTMTAPPEEISRVLAEVGEFCEQRPKGCARVLGVHLE 120

Query: 121 GPYINPGKLGAQPNFAHTALMAEVEAYLALAPIRVITIAPEIAGHDKLIRALSDRGIRMQ 180
           GPYINPGKLGAQPNFAHTALMAEVEAYLALAPIRVITIAPEIAGHDKLIRALSDRGIRMQ
Sbjct: 121 GPYINPGKLGAQPNFAHTALMAEVEAYLALAPIRVITIAPEIAGHDKLIRALSDRGIRMQ 180

Query: 181 IGHTLGSYEEGVAALEAGASSFTHLYNAMSPLHHREPGIVGAALAHAKYAELIPDLLHVH 240
           IGHTLGSYEEGVAALEAGASSFTHLYNAMSPLHHREPGIVGAALAHAKYAELIPDLLHVH
Sbjct: 181 IGHTLGSYEEGVAALEAGASSFTHLYNAMSPLHHREPGIVGAALAHAKYAELIPDLLHVH 240

Query: 241 PGAIRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLPDGTLAGSTLTMD 300
           PGAIRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLPDGTLAGSTLTMD
Sbjct: 241 PGAIRVALRSIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLPDGTLAGSTLTMD 300

Query: 301 QALRNLVKIGLPLAEASQRLSQFPADYLGIQERGRLQPGAWADCVRLDRSLTLTAVMVEG 360
           QALRNLVKIGLPLAEASQRLSQFPADYLGIQERGRLQPGAWADCVRLDRSLTLTAVMVEG
Sbjct: 301 QALRNLVKIGLPLAEASQRLSQFPADYLGIQERGRLQPGAWADCVRLDRSLTLTAVMVEG 360

Query: 361 EDIDFKNA 368
           EDIDFKNA
Sbjct: 361 EDIDFKNA 368


Lambda     K      H
   0.320    0.138    0.416 

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: 716
Number of extensions: 19
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: 368
Length of database: 368
Length adjustment: 30
Effective length of query: 338
Effective length of database: 338
Effective search space:   114244
Effective search space used:   114244
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_04450 AO353_04450 (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.32400.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
    1.1e-79  254.1   0.0    1.3e-79  253.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450  AO353_04450 N-acetylglucosamine-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450  AO353_04450 N-acetylglucosamine-6-phosphate deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  253.8   0.0   1.3e-79   1.3e-79      52     379 ..      40     360 ..      15     361 .. 0.94

  Alignments for each domain:
  == domain 1  score: 253.8 bits;  conditional E-value: 1.3e-79
                                     TIGR00221  52 nvltpGliDvqlnGcgGvdtndasvetleimsealaksGvtsfLptlitredeeikkavkvarey 116
                                                    +l+pG+iD++++G+gG d+++ +  +++ + ++  + G+ts L+t++t++ eei++ +  + e+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450  40 PYLLPGFIDLHVHGGGGKDIMEGT-PAFDTITKTHVRFGTTSLLATTMTAPPEEISRVLAEVGEF 103
                                                   589******************854.67788889999***************************** PP

                                     TIGR00221 117 lakekn..akiLGlhleGPflslekkGahpkeyirepdvellkkfldeagdvitkvtlapeekqt 179
                                                     + +   a++LG+hleGP++++ k Ga+p ++ + + ++ ++ +l  a   i+ +t+ape  ++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450 104 CEQRPKgcARVLGVHLEGPYINPGKLGAQP-NFAHTALMAEVEAYLALA--PIRVITIAPEIAGH 165
                                                   *9998879********************86.788887666658888766..6************* PP

                                     TIGR00221 180 aelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGavLdeddvv 244
                                                    +li+ l + gi +++Ght   yee  +a +aG++  thlynams+l+hRepg++Ga+L++   +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450 166 DKLIRALSDRGIRMQIGHTLGSYEEGVAALEAGASSFTHLYNAMSPLHHREPGIVGAALAH-AKY 229
                                                   *************************************************************.679 PP

                                     TIGR00221 245 teiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyiredtlldkngtl 309
                                                   +e+i D lh+hp +ir+a +   +  l  vtDs+aaag++++++  + ++v+   +++   +gtl
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450 230 AELIPDLLHVHPGAIRVALR--SIPCLYCVTDSTAAAGMPDGEYKLGSHTVTKCLGGVRLPDGTL 292
                                                   ****************9966..5566*************************************** PP

                                     TIGR00221 310 aGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfevil 374
                                                   aGs+ltm ++++nlv  + ++l+++ +  s++pa  lgi++r G ++ G  a+ + l++   ++ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450 293 AGSTLTMDQALRNLVKIG-LPLAEASQRLSQFPADYLGIQER-GRLQPGAWADCVRLDRSLTLTA 355
                                                   ****************99.***********************.********************** PP

                                     TIGR00221 375 tiveg 379
                                                    +veg
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_04450 356 VMVEG 360
                                                   ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (368 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: 10.55
//
[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:

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