GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Psychromonas ossibalaenae JAMM 0738

Align N-acetylglucosamine-6-phosphate deacetylase subunit (EC 3.5.1.25) (characterized)
to candidate WP_019615253.1 G327_RS0113170 N-acetylglucosamine-6-phosphate deacetylase

Query= metacyc::MONOMER-13103
         (383 letters)



>NCBI__GCF_000381745.1:WP_019615253.1
          Length = 382

 Score =  266 bits (681), Expect = 6e-76
 Identities = 146/375 (38%), Positives = 223/375 (59%), Gaps = 7/375 (1%)

Query: 7   ADQFFYPQGIRQGGYLELIDGKFGKLVQSVPQDAEVIDYSGYSIAPGLVDTHIHGFGGVD 66
           AD+ F   GI +   + + +GK   + +++P D E+I   G S+ PG +D HIHG  G D
Sbjct: 7   ADRVFGAAGIEKNTAVVVENGKITAVTENIPTDCELIKLEGLSLLPGFIDIHIHGRDGAD 66

Query: 67  VMDNNIEGSLHTMSEGLLTTGVTSFLPTTLTSSYERLLAVTENIGA--RYQEASGAKIRG 124
           VMD + + +L  +++ L  TGV  ++ TT+T+ ++ +L     + +  R ++  GA++ G
Sbjct: 67  VMDAS-QSALQNIADALPETGVVGWVGTTVTAPWQDILDSLAAVRSFTRKEQTQGAQLLG 125

Query: 125 LYFEGPYFTEKYKGAQNPAYMKDPSMDEFRAWQKAANGLLNKIALAPERDGVEDFVRTLT 184
            + EGPYFTE ++G+  PAY+K P++ E    ++AA   L + A+APE  G  + VR LT
Sbjct: 126 SFLEGPYFTEPHRGSHPPAYLKSPTISELVELKEAAGSSLIRAAVAPEGTGAMEAVRWLT 185

Query: 185 DEGVTVALGHSNATYDEAKTAVEAGASVWVHAYNGMRGLTHRELGMVGAMYELPH-TYAE 243
           + G+  ++ H++AT+++   A   GA   VH +NGM GL HR+ G  GA+  L H   AE
Sbjct: 186 ENGIKTSVAHTDATFEQVTEAFHLGADCGVHLFNGMSGLHHRQPGCCGAV--LYHDMLAE 243

Query: 244 LICDGHHVDPKACDILLKQKGHENIALITDCMTAGGLEDGDYMLGEFPVVVAEGTARLKS 303
           LI DG HV+P    +  + KG++ IALITDCM AGGL DGDY LG   + V +G AR   
Sbjct: 244 LIADGIHVNPVMMQLAYRMKGYQGIALITDCMRAGGLADGDYQLGAQVITVTDGEAR-SP 302

Query: 304 TGNLAGSILKLKDGLKNVVKWGIANPHQAVMMASLIPAKSVHIDDVCGQIMEGYDADFIV 363
            G+LAGS   L   L+N+V        +AV MAS +PAK + I+   G I  G DA F +
Sbjct: 303 CGSLAGSTCSLDQALRNMVFKSDVPQWEAVQMASAVPAKYLGIEHRLGSIAPGLDASFTI 362

Query: 364 LDKDLELVATYLDGQ 378
           +D +L++  T ++G+
Sbjct: 363 MDNELQVQGTIINGE 377


Lambda     K      H
   0.318    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: 416
Number of extensions: 28
Number of successful extensions: 5
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: 383
Length of database: 382
Length adjustment: 30
Effective length of query: 353
Effective length of database: 352
Effective search space:   124256
Effective search space used:   124256
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_019615253.1 G327_RS0113170 (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.3816415.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.1e-99  318.0   0.0    4.6e-99  317.9   0.0    1.0  1  NCBI__GCF_000381745.1:WP_019615253.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381745.1:WP_019615253.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.9   0.0   4.6e-99   4.6e-99       4     379 ..       2     376 ..       1     377 [. 0.98

  Alignments for each domain:
  == domain 1  score: 317.9 bits;  conditional E-value: 4.6e-99
                             TIGR00221   4 slllkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv 76 
                                            ++l+  +++    + +++avv++++ki+av+  ++ +++ + i+l+g  l+pG+iD++++G  G+d++das 
  NCBI__GCF_000381745.1:WP_019615253.1   2 RYALIADRVFGAAGIEKNTAVVVENGKITAVT--ENIPTDCELIKLEGLSLLPGFIDIHIHGRDGADVMDASQ 72 
                                           6899999999999999*************996..56789999******************************* PP

                             TIGR00221  77 etleimsealaksGvtsfLptlitredeeikkavkvareylakekn..akiLGlhleGPflslekkGahpkey 147
                                           ++l+ + +al++ Gv++++ t++t++ ++i  ++ ++r +  ke+   a++LG  leGP++   ++G hp+ y
  NCBI__GCF_000381745.1:WP_019615253.1  73 SALQNIADALPETGVVGWVGTTVTAPWQDILDSLAAVRSFTRKEQTqgAQLLGSFLEGPYFTEPHRGSHPPAY 145
                                           ******************************************998777************************* PP

                             TIGR00221 148 irepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathly 220
                                           ++ p++  l+++ ++ag  + +  +ape ++ +e ++ l+e+gi  s+ ht+at+e+++eaf+ G+    hl+
  NCBI__GCF_000381745.1:WP_019615253.1 146 LKSPTISELVELKEAAGSSLIRAAVAPEGTGAMEAVRWLTENGIKTSVAHTDATFEQVTEAFHLGADCGVHLF 218
                                           ******999**************************************************************** PP

                             TIGR00221 221 namskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGk 293
                                           n ms l+hR+pg  GavL + d+ +e+iaDG+h++p  ++la ++kg   + l+tD ++a g+ ++ ++ + +
  NCBI__GCF_000381745.1:WP_019615253.1 219 NGMSGLHHRQPGCCGAVLYH-DMLAELIADGIHVNPVMMQLAYRMKGYQGIALITDCMRAGGLADGDYQLGAQ 290
                                           ********************.**************************************************** PP

                             TIGR00221 294 evyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavl 366
                                            +++ ++++    g laGs+  + ++++n+v  ++++  ++v+++s  pa+ lgi++rlGs+a G da  +++
  NCBI__GCF_000381745.1:WP_019615253.1 291 VITVTDGEARSPCGSLAGSTCSLDQALRNMVFKSDVPQWEAVQMASAVPAKYLGIEHRLGSIAPGLDASFTIM 363
                                           ************************************************************************* PP

                             TIGR00221 367 tkdfeviltiveg 379
                                           +++ +v++ti++g
  NCBI__GCF_000381745.1:WP_019615253.1 364 DNELQVQGTIING 376
                                           ************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (382 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: 28.08
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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