Alignments for a candidate for nagA in Klebsiella michiganensis M5al

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.26211.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: 9.48
//
[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