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

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.7615.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: 00:00:00.02
# Mc/sec: 7.26
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources