GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagA in Klebsiella michiganensis M5al

Align N-acetylglucosamine 6-phosphate deacetylase (NagA;b0677) (EC 3.5.1.25) (characterized)
to candidate BWI76_RS08210 BWI76_RS08210 N-acetylglucosamine-6-phosphate deacetylase

Query= CAZy::AAC73771.1
         (382 letters)



>FitnessBrowser__Koxy:BWI76_RS08210
          Length = 382

 Score =  679 bits (1752), Expect = 0.0
 Identities = 331/382 (86%), Positives = 360/382 (94%)

Query: 1   MYALTQGRIFTGHEFLDDHAVVIADGLIKSVCPVAELPPEIEQRSLNGAILSPGFIDVQL 60
           MYALTQGRI+TGHE LDDHA+VIA+GLI+ +CP  ELP  IEQRS+NGAIL+PGFIDVQL
Sbjct: 1   MYALTQGRIYTGHEILDDHAIVIANGLIERICPQTELPTGIEQRSVNGAILAPGFIDVQL 60

Query: 61  NGCGGVQFNDTAEAVSVETLEIMQKANEKSGCTNYLPTLITTSDELMKQGVRVMREYLAK 120
           NGCGGVQFNDTA+AV+VETLEIMQKANE+SGCT+YLPTLIT SD+LMKQGVRVMREYL K
Sbjct: 61  NGCGGVQFNDTADAVTVETLEIMQKANERSGCTSYLPTLITASDDLMKQGVRVMREYLQK 120

Query: 121 HPNQALGLHLEGPWLNLVKKGTHNPNFVRKPDAALVDFLCENADVITKVTLAPEMVPAEV 180
           HPNQALGLHLEGPWLN+VKKGTHNP++VRKPDAALVDFLCENADVITK+TLAPE V  +V
Sbjct: 121 HPNQALGLHLEGPWLNIVKKGTHNPDYVRKPDAALVDFLCENADVITKITLAPERVEPDV 180

Query: 181 ISKLANAGIVVSAGHSNATLKEAKAGFRAGITFATHLYNAMPYITGREPGLAGAILDEAD 240
           I KL  AGI+VSAGHSNATLKEAK GFRAGITFATHL+NAMPYITGREPGLAGAI DE D
Sbjct: 181 IRKLVAAGIIVSAGHSNATLKEAKIGFRAGITFATHLFNAMPYITGREPGLAGAIFDEPD 240

Query: 241 IYCGIIADGLHVDYANIRNAKRLKGDKLCLVTDATAPAGANIEQFIFAGKTIYYRNGLCV 300
           +YCGII DG+HVDYAN+R AKRLKGDKLCLVTDATAPAGANIEQFIFAGKTIYYRNGLCV
Sbjct: 241 VYCGIIVDGMHVDYANVRLAKRLKGDKLCLVTDATAPAGANIEQFIFAGKTIYYRNGLCV 300

Query: 301 DENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYPARAIGVEKRLGTLAAGKVANL 360
           DENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYP+RAIGV+K+LG++A G VANL
Sbjct: 301 DENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYPSRAIGVDKQLGSIAPGMVANL 360

Query: 361 TAFTPDFKITKTIVNGNEVVTQ 382
           TAFT D+KITKTIVNGNEVVT+
Sbjct: 361 TAFTRDYKITKTIVNGNEVVTE 382


Lambda     K      H
   0.319    0.136    0.396 

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: 617
Number of extensions: 9
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: 382
Length of database: 382
Length adjustment: 30
Effective length of query: 352
Effective length of database: 352
Effective search space:   123904
Effective search space used:   123904
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate BWI76_RS08210 BWI76_RS08210 (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.2833.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.6e-178  578.7   0.1     3e-178  578.5   0.1    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS08210  BWI76_RS08210 N-acetylglucosamin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS08210  BWI76_RS08210 N-acetylglucosamine-6-phosphate deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  578.5   0.1    3e-178    3e-178       4     380 .]       1     377 [.       1     377 [. 0.99

  Alignments for each domain:
  == domain 1  score: 578.5 bits;  conditional E-value: 3e-178
                               TIGR00221   4 slllkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtnd. 73 
                                             +++l++ +i+t++++ldd+a+vi++++i+ ++++ el+++i++++++g++l+pG+iDvqlnGcgGv++nd 
  lcl|FitnessBrowser__Koxy:BWI76_RS08210   1 MYALTQGRIYTGHEILDDHAIVIANGLIERICPQTELPTGIEQRSVNGAILAPGFIDVQLNGCGGVQFNDt 71 
                                             69********************************************************************6 PP

                               TIGR00221  74 ...asvetleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkG 141
                                                 +vetleim++a+++sG+ts+Lptlit++d+ +k++v+v+reyl k++n ++LGlhleGP+l+++kkG
  lcl|FitnessBrowser__Koxy:BWI76_RS08210  72 adaVTVETLEIMQKANERSGCTSYLPTLITASDDLMKQGVRVMREYLQKHPN-QALGLHLEGPWLNIVKKG 141
                                             654455**********************************************.****************** PP

                               TIGR00221 142 ahpkeyirepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaG 212
                                             +h+++y+r+pd++l ++fl+e++dvitk+tlap e+++ ++i+kl+ agiivsaGh+nat++e+k +f+aG
  lcl|FitnessBrowser__Koxy:BWI76_RS08210 142 THNPDYVRKPDAAL-VDFLCENADVITKITLAP-ERVEPDVIRKLVAAGIIVSAGHSNATLKEAKIGFRAG 210
                                             **************.******************.99999******************************** PP

                               TIGR00221 213 itfathlynamskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaaga 283
                                             itfathl+nam+++++Repg++Ga+ de dv+++ii+DG+h++++n+rlak+lkgd kl+lvtD++a+aga
  lcl|FitnessBrowser__Koxy:BWI76_RS08210 211 ITFATHLFNAMPYITGREPGLAGAIFDEPDVYCGIIVDGMHVDYANVRLAKRLKGD-KLCLVTDATAPAGA 280
                                             ********************************************************.************** PP

                               TIGR00221 284 klekfifaGkevyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGs 354
                                             ++e+fifaGk++y+r++ ++d+ngtl+Gssltmiegv+nlve+++i+l++v+r+++l+p+ra+g+d++lGs
  lcl|FitnessBrowser__Koxy:BWI76_RS08210 281 NIEQFIFAGKTIYYRNGLCVDENGTLSGSSLTMIEGVRNLVEHCGIALDEVLRMATLYPSRAIGVDKQLGS 351
                                             *********************************************************************** PP

                               TIGR00221 355 vakGkdanLavltkdfeviltivegk 380
                                             +a G +anL+++t+d+++++tiv+g+
  lcl|FitnessBrowser__Koxy:BWI76_RS08210 352 IAPGMVANLTAFTRDYKITKTIVNGN 377
                                             ************************97 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.67
//
[ok]

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

Links

Downloads

Related tools

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