GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Shewanella oneidensis MR-1

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate 202606 SO3505 N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file)

Query= reanno::MR1:202606
         (378 letters)



>FitnessBrowser__MR1:202606
          Length = 378

 Score =  745 bits (1924), Expect = 0.0
 Identities = 378/378 (100%), Positives = 378/378 (100%)

Query: 1   MKFTLIAEQLFDGESFHQDVPVTIEDGLIASFDTALGAKEVRYTGTLVPGFIDVQVNGGG 60
           MKFTLIAEQLFDGESFHQDVPVTIEDGLIASFDTALGAKEVRYTGTLVPGFIDVQVNGGG
Sbjct: 1   MKFTLIAEQLFDGESFHQDVPVTIEDGLIASFDTALGAKEVRYTGTLVPGFIDVQVNGGG 60

Query: 61  GALFNTSPTVACIETIGKAHARFGTTGFLPTLITDNVQVMAKAADAVALAVAQKSAGVLG 120
           GALFNTSPTVACIETIGKAHARFGTTGFLPTLITDNVQVMAKAADAVALAVAQKSAGVLG
Sbjct: 61  GALFNTSPTVACIETIGKAHARFGTTGFLPTLITDNVQVMAKAADAVALAVAQKSAGVLG 120

Query: 121 VHFEGPHLSVPKKGVHPQGFIREITEAELAIFCRQDLGIRVVTLAPENVSPEVIRLLVES 180
           VHFEGPHLSVPKKGVHPQGFIREITEAELAIFCRQDLGIRVVTLAPENVSPEVIRLLVES
Sbjct: 121 VHFEGPHLSVPKKGVHPQGFIREITEAELAIFCRQDLGIRVVTLAPENVSPEVIRLLVES 180

Query: 181 GVKVCLGHSNADYDTVVAALKAGATGFTHLYNAMSPLGSREPGVVGAAIESETAWCGLIV 240
           GVKVCLGHSNADYDTVVAALKAGATGFTHLYNAMSPLGSREPGVVGAAIESETAWCGLIV
Sbjct: 181 GVKVCLGHSNADYDTVVAALKAGATGFTHLYNAMSPLGSREPGVVGAAIESETAWCGLIV 240

Query: 241 DGHHVHPAAARIALRAKPRGKMMLVTDAMPPVGMDDETSFELFGTQVLRVGDRLNAVTGE 300
           DGHHVHPAAARIALRAKPRGKMMLVTDAMPPVGMDDETSFELFGTQVLRVGDRLNAVTGE
Sbjct: 241 DGHHVHPAAARIALRAKPRGKMMLVTDAMPPVGMDDETSFELFGTQVLRVGDRLNAVTGE 300

Query: 301 LAGCVLDMASAVHNTVNMLGLPLGEALRMAALYPAEFLGIADSVGRLAVGQRADLVLLDN 360
           LAGCVLDMASAVHNTVNMLGLPLGEALRMAALYPAEFLGIADSVGRLAVGQRADLVLLDN
Sbjct: 301 LAGCVLDMASAVHNTVNMLGLPLGEALRMAALYPAEFLGIADSVGRLAVGQRADLVLLDN 360

Query: 361 QYQVLANYIAGNAVYVRP 378
           QYQVLANYIAGNAVYVRP
Sbjct: 361 QYQVLANYIAGNAVYVRP 378


Lambda     K      H
   0.321    0.137    0.400 

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: 634
Number of extensions: 18
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: 378
Length of database: 378
Length adjustment: 30
Effective length of query: 348
Effective length of database: 348
Effective search space:   121104
Effective search space used:   121104
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 202606 SO3505 (N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file))
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.1964277.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    1.4e-95  306.4   0.0    1.6e-95  306.2   0.0    1.0  1  lcl|FitnessBrowser__MR1:202606  SO3505 N-acetylglucosamine-6-pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202606  SO3505 N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.2   0.0   1.6e-95   1.6e-95       5     380 .]       3     372 ..       1     372 [. 0.92

  Alignments for each domain:
  == domain 1  score: 306.2 bits;  conditional E-value: 1.6e-95
                       TIGR00221   5 lllkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv.etleim 82 
                                     + l+  +++ ++ + +d  v i+d++i +  t      + ke+   g +l pG+iDvq+nG+gG+ +n   +   +e +
  lcl|FitnessBrowser__MR1:202606   3 FTLIAEQLFDGESFHQDVPVTIEDGLIASFDTAL----GAKEVRYTG-TLVPGFIDVQVNGGGGALFNTSPTvACIETI 76 
                                     566777888899999999********99987764....455566555.699*****************96554****** PP

                       TIGR00221  83 sealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirepdvellkkfld 161
                                      +a a+ G+t+fLptlit + + + ka  ++  ++a +k+a +LG+h+eGP+ls+ kkG+hp+ +ire++ + l  + +
  lcl|FitnessBrowser__MR1:202606  77 GKAHARFGTTGFLPTLITDNVQVMAKAADAVALAVA-QKSAGVLGVHFEGPHLSVPKKGVHPQGFIREITEAEL-AIFC 153
                                     ***************************998876665.5677***************************986553.5666 PP

                       TIGR00221 162 eagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRepgviGavLde 240
                                          i+ vtlap e++  e+i+ l+e g+ v +Gh+na+y+++ +a kaG+t  thlynams+l  Repgv+Ga++++
  lcl|FitnessBrowser__MR1:202606 154 RQDLGIRVVTLAP-ENVSPEVIRLLVESGVKVCLGHSNADYDTVVAALKAGATGFTHLYNAMSPLGSREPGVVGAAIES 231
                                     67777********.99*************************************************************** PP

                       TIGR00221 241 ddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagakle.kfifaGkevyiredtlldkngtlaGssltmie 318
                                     +   +++i+DG+h+hp+++r+a ++k   k++lvtD++ + g+++e +f+  G +v   +d+l    g laG +l m  
  lcl|FitnessBrowser__MR1:202606 232 ETAWCGLIVDGHHVHPAAARIALRAKPRGKMMLVTDAMPPVGMDDEtSFELFGTQVLRVGDRLNAVTGELAGCVLDMAS 310
                                     *******************************************96538******************************* PP

                       TIGR00221 319 gvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfeviltivegk 380
                                     +v+n v+  +++l +++r+++l+pa  lgi d  G +a+G+ a+L++l+++++v    + g+
  lcl|FitnessBrowser__MR1:202606 311 AVHNTVNMLGLPLGEALRMAALYPAEFLGIADSVGRLAVGQRADLVLLDNQYQVLANYIAGN 372
                                     ******************************************************98888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (378 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 22.62
//
[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