GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Sporolactobacillus vineae SL153

Align N-acetylglucosamine 6-phosphate deacetylase (NagA;BSU35010) (EC 3.5.1.25) (characterized)
to candidate WP_010631270.1 RH97_RS05120 N-acetylglucosamine-6-phosphate deacetylase

Query= CAZy::CAB15506.1
         (396 letters)



>NCBI__GCF_000246965.1:WP_010631270.1
          Length = 391

 Score =  341 bits (875), Expect = 2e-98
 Identities = 183/385 (47%), Positives = 250/385 (64%), Gaps = 3/385 (0%)

Query: 11  AIVTENEVIKNGYVGINDGKISTVSTERPKEPYSKEIQAPADSVLLPGMIDIHIHGGYGA 70
           +I + ++ I+NG +  + GKI  V     ++P  K IQ PA    +PGMID+HIHG   A
Sbjct: 9   SIYSNHDWIENGTLTFDHGKIVGVGHSL-EQPGDKVIQFPAGYKCIPGMIDMHIHGANAA 67

Query: 71  DTMDASFSTLDIMSSRLPEEGTTSFLATTITQEHGNISQALVNAREWKAAEESSLLGAEL 130
           DTMDA+   L  ++S LPEE TTSFLATTITQ    I  AL NA E    ++     AE+
Sbjct: 68  DTMDATHEALSTIASVLPEEATTSFLATTITQSEEAIQAALKNAAEVIGHQKPG--EAEI 125

Query: 131 LGIHLEGPFVSPKRAGAQPKEWIRPSDVELFKKWQQEAGGLIKIVTLAPEEDQHFELIRH 190
           LG+HLEGPF+S ++ GAQP+E+I  +D E F  WQ+ +G  I+ VTLAPE     ELIRH
Sbjct: 126 LGVHLEGPFISKEKCGAQPEEYISDADTERFDNWQKLSGNHIREVTLAPEIKGGMELIRH 185

Query: 191 LKDESIIASMGHTDADSALLSDAAKAGASHMTHLYNAMSPFHHREPGVIGTALAHDGFVT 250
           L  + ++AS+GH++     +  A  AGA+ +TH+YN M   HHREPG++G AL H G  T
Sbjct: 186 LAAQGVVASIGHSNGYDEDVIRAIDAGATQVTHVYNGMRGMHHREPGILGGALLHHGLYT 245

Query: 251 ELIADGIHSHPLAAKLAFLAKGSSKLILITDSMRAKGLKDGVYEFGGQSVTVRGRTALLS 310
           ELI DG H       LA+  KGS ++ILITD+MRAK LK+G Y+ GGQ V V+   A+LS
Sbjct: 246 ELICDGKHVCQGMVNLAYKLKGSDRMILITDAMRAKCLKNGTYDLGGQEVHVKDGLAVLS 305

Query: 311 DGTLAGSILKMNEGARHMREFTNCSWTDIANITSENAAKQLGIFDRKGSVTVGKDADLVI 370
            GT+AGS+LKM++  R+M  FT+ +  DI  + + N A Q  +FDRKGS+ +GKDAD ++
Sbjct: 306 SGTIAGSVLKMDQAFRNMLAFTDATIEDIVQMGAINPALQCNVFDRKGSLEIGKDADFIV 365

Query: 371 VSSDCEVILTICRGNIAFISKEADQ 395
           +  + ++ LT+CRG IA+  KE  Q
Sbjct: 366 LDKNNQLALTVCRGEIAYQRKEIVQ 390


Lambda     K      H
   0.316    0.132    0.377 

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: 417
Number of extensions: 13
Number of successful extensions: 2
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: 396
Length of database: 391
Length adjustment: 31
Effective length of query: 365
Effective length of database: 360
Effective search space:   131400
Effective search space used:   131400
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_010631270.1 RH97_RS05120 (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.2173177.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.3e-117  377.2   4.1   4.8e-117  377.0   4.1    1.0  1  NCBI__GCF_000246965.1:WP_010631270.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000246965.1:WP_010631270.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.0   4.1  4.8e-117  4.8e-117       8     379 ..       6     379 ..       1     380 [. 0.97

  Alignments for each domain:
  == domain 1  score: 377.0 bits;  conditional E-value: 4.8e-117
                             TIGR00221   8 kdkailtendvlddsavvindekikavvteaeleeeikeidlkg.nvltpGliDvqlnGcgGvdtndasvetl 79 
                                             ++i+ ++d ++++    + +ki  v  + e +++ k i+ ++     pG+iD++++G++ +dt+da+ e+l
  NCBI__GCF_000246965.1:WP_010631270.1   6 VGCSIYSNHDWIENGTLTFDHGKIVGVGHSLE-QPGDKVIQFPAgYKCIPGMIDMHIHGANAADTMDATHEAL 77 
                                           5699*********************9987766.5788999999857799************************ PP

                             TIGR00221  80 eimsealaksGvtsfLptlitredeeikkavkvareylakekn..akiLGlhleGPflslekkGahpkeyire 150
                                             + + l+++ +tsfL+t+it+++e i+ a+k+a e ++ +k   a+iLG+hleGPf+s ek Ga+p+eyi +
  NCBI__GCF_000246965.1:WP_010631270.1  78 STIASVLPEEATTSFLATTITQSEEAIQAALKNAAEVIGHQKPgeAEILGVHLEGPFISKEKCGAQPEEYISD 150
                                           ***************************************998778**************************** PP

                             TIGR00221 151 pdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynam 223
                                           +d e + ++++ +g++i+ vtlape k+ +eli++l+ +g+++s+Gh+n   e ++ a+ aG+t +th+yn m
  NCBI__GCF_000246965.1:WP_010631270.1 151 ADTERFDNWQKLSGNHIREVTLAPEIKGGMELIRHLAAQGVVASIGHSNGYDEDVIRAIDAGATQVTHVYNGM 223
                                           ************************************************************************* PP

                             TIGR00221 224 skldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevy 296
                                             ++hRepg++G +L + +++te+i DG h+    + la klkg+ +++l+tD+++a+++k +++  +G+ev 
  NCBI__GCF_000246965.1:WP_010631270.1 224 RGMHHREPGILGGALLHHGLYTELICDGKHVCQGMVNLAYKLKGSDRMILITDAMRAKCLKNGTYDLGGQEVH 296
                                           ************************************************************************* PP

                             TIGR00221 297 iredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkd 369
                                           ++++ ++ ++gt+aGs+l+m ++ +n++ f++ +++d+v++ + npa + +++dr+Gs++ Gkda+  vl+k+
  NCBI__GCF_000246965.1:WP_010631270.1 297 VKDGLAVLSSGTIAGSVLKMDQAFRNMLAFTDATIEDIVQMGAINPALQCNVFDRKGSLEIGKDADFIVLDKN 369
                                           ************************************************************************* PP

                             TIGR00221 370 feviltiveg 379
                                            ++ lt+++g
  NCBI__GCF_000246965.1:WP_010631270.1 370 NQLALTVCRG 379
                                           ********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (391 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: 16.81
//
[ok]

This GapMind analysis is from Sep 24 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