GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Bacteroides thetaiotaomicron VPI-5482

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate 350203 BT0675 N-acetylglucosamine-6-phosphate deacetylase (NCBI ptt file)

Query= BRENDA::Q8Y5F6
         (377 letters)



>FitnessBrowser__Btheta:350203
          Length = 388

 Score =  206 bits (523), Expect = 1e-57
 Identities = 116/338 (34%), Positives = 192/338 (56%), Gaps = 11/338 (3%)

Query: 45  DGNGRLLIPGMIDVHIHGAKNYDMMDGSTESIQAVSMACAETGCTSFLVTSVSSSLEDLI 104
           D  G  ++PG +++H+HG    D M+G+ ++ +    A  + G TS   T +SSS   +I
Sbjct: 46  DAKGMYIVPGGVEIHVHGGGGRDFMEGTEDAFRTAIKAHMQHGTTSIFPT-LSSSTIPMI 104

Query: 105 QMIRQTKKVIGKEKGAKIAGIHLEGPYLNIEKKGMQNPAHLRHPDLKEMKKIFDEADGLI 164
           +   +T + +  E  + + G+HLEG Y N+E  G Q P ++++PD +E   + +E    I
Sbjct: 105 RAAAETTEKMMAEPDSPVLGLHLEGHYFNMEMAGGQIPENIKNPDPEEYIPLLEETH-CI 163

Query: 165 KMVTIAPELPGGIELIDFLKKRGVVVAIAHSNATYEEAQDAFEKGASHITHCFNAMPAIH 224
           K    APELPG ++   ++  +GV+ ++ H+ A +E+ Q A+E G +H TH +NAMP  H
Sbjct: 164 KRWDAAPELPGAMQFGKYITAKGVLASVGHTQAEFEDIQTAYEAGYTHATHFYNAMPGFH 223

Query: 225 HRA----PGLVAAALENDSISVQAIVDGVHLHPGIVRLIHKIKGPDKMVLTTDALQAMGV 280
            R      G V +    D ++V+ + DG+H+ P I+RL++KIKG ++  L TDAL A   
Sbjct: 224 KRKEYKYEGTVESIYLIDDMTVEVVADGIHVPPTILRLVYKIKGVERTCLITDAL-ACAA 282

Query: 281 GDGEYIFGGHQVTVTEGVARLQD-GTLASSTVTMNKSLR-LSNEFGINLQDTIQMATSTP 338
            D +  F   +V + +GV +L D   LA S  TM++ +R +     I L D ++MA+ TP
Sbjct: 283 SDSKTAF-DPRVIIEDGVCKLADRSALAGSVATMDRLIRTMVQNAEIPLADAVRMASETP 341

Query: 339 ADILG-MKNLGRIEKGYSADLVLLDKKFEVLSTWINGE 375
           A I+G +   G +E+G  AD++ LD+   V + W  G+
Sbjct: 342 ARIMGVLDRKGTLERGKDADIIALDRDLNVRAVWAMGQ 379


Lambda     K      H
   0.317    0.134    0.380 

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: 358
Number of extensions: 19
Number of successful extensions: 6
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: 377
Length of database: 388
Length adjustment: 30
Effective length of query: 347
Effective length of database: 358
Effective search space:   124226
Effective search space used:   124226
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 350203 BT0675 (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.8617.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-83  267.2   0.1    1.3e-83  267.0   0.1    1.0  1  lcl|FitnessBrowser__Btheta:350203  BT0675 N-acetylglucosamine-6-pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350203  BT0675 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 !  267.0   0.1   1.3e-83   1.3e-83       6     374 ..       4     373 ..       1     379 [. 0.91

  Alignments for each domain:
  == domain 1  score: 267.0 bits;  conditional E-value: 1.3e-83
                          TIGR00221   6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasvetlei 81 
                                         +++ +ilt +  l+d+ v+i+d ki +v+  +    + k id+kg ++ pG ++++++G+gG d+++ + +++  
  lcl|FitnessBrowser__Btheta:350203   4 QIINARILTPQGWLKDGSVLIRDHKILEVTNCDLAVIGAKLIDAKGMYIVPGGVEIHVHGGGGRDFMEGTEDAFRT 79 
                                        58899*************************999999**************************************** PP

                          TIGR00221  82 msealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyirepdvellk 157
                                          +a  ++G+ts  ptl +  +  i+ a +++ e + +e+++ +LGlhleG ++++e +G + +e i++pd+e + 
  lcl|FitnessBrowser__Btheta:350203  80 AIKAHMQHGTTSIFPTLSSSTIPMIRAAAETT-EKMMAEPDSPVLGLHLEGHYFNMEMAGGQIPENIKNPDPEEYI 154
                                        *****************999887776666655.555556666*******************************977 PP

                          TIGR00221 158 kfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynamskldhRe... 230
                                         +l+e +  i++   ape+ + +++ + ++ +g+ +s+Ght+a++e ++ a++aG t+ath+ynam+ +++R+   
  lcl|FitnessBrowser__Btheta:350203 155 PLLEE-THCIKRWDAAPELPGAMQFGKYITAKGVLASVGHTQAEFEDIQTAYEAGYTHATHFYNAMPGFHKRKeyk 229
                                        77765.689*************************************************************885233 PP

                          TIGR00221 231 .pgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevyiredtlld. 304
                                          g + ++   dd+++e++aDG+h+ p+ +rl  k+kg  + +l+tD+la a    ++ ++    v i+++ +   
  lcl|FitnessBrowser__Btheta:350203 230 yEGTVESIYLIDDMTVEVVADGIHVPPTILRLVYKIKGVERTCLITDALACA--ASDSKTAFDPRVIIEDGVCKLa 303
                                        346777777889************************************9754..5555566678899999999874 PP

                          TIGR00221 305 kngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkdfevil 374
                                        +   laGs+ tm   ++ +v  +ei+l+d+vr++s+ par++g+ dr+G++++Gkda++ +l++d +v  
  lcl|FitnessBrowser__Btheta:350203 304 DRSALAGSVATMDRLIRTMVQNAEIPLADAVRMASETPARIMGVLDRKGTLERGKDADIIALDRDLNVRA 373
                                        6689***************************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (388 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.15
//
[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