Alignments for a candidate for nagA in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Caulobacter crescentus NA1000

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate CCNA_00452 CCNA_00452 N-acetylglucosamine-6-phosphate deacetylase

Query= reanno::Caulo:CCNA_00452
         (378 letters)



>FitnessBrowser__Caulo:CCNA_00452
          Length = 378

 Score =  745 bits (1923), Expect = 0.0
 Identities = 378/378 (100%), Positives = 378/378 (100%)

Query: 1   MPAALINGRVLTESGVVEGKAVLVKDGLILDVIEAAQTPSDAKPRDLKGGLLVPGFIDTQ 60
           MPAALINGRVLTESGVVEGKAVLVKDGLILDVIEAAQTPSDAKPRDLKGGLLVPGFIDTQ
Sbjct: 1   MPAALINGRVLTESGVVEGKAVLVKDGLILDVIEAAQTPSDAKPRDLKGGLLVPGFIDTQ 60

Query: 61  VNGGGGVLFNDAPTVETIATIGAAHRRFGTTGFLPTLISDDLRVVDQAMRATEEAIARGV 120
           VNGGGGVLFNDAPTVETIATIGAAHRRFGTTGFLPTLISDDLRVVDQAMRATEEAIARGV
Sbjct: 61  VNGGGGVLFNDAPTVETIATIGAAHRRFGTTGFLPTLISDDLRVVDQAMRATEEAIARGV 120

Query: 121 PGVLGLHIEGPFLNPKRKGIHDAGKFRVIDDEALALLTSLKRGKTLVTLAPERTTPQIIR 180
           PGVLGLHIEGPFLNPKRKGIHDAGKFRVIDDEALALLTSLKRGKTLVTLAPERTTPQIIR
Sbjct: 121 PGVLGLHIEGPFLNPKRKGIHDAGKFRVIDDEALALLTSLKRGKTLVTLAPERTTPQIIR 180

Query: 181 RLADAGVIVAAGHTNALYATMRQALEHGLTGFTHLFNAMSPLTSREPGAVGAALESPDAW 240
           RLADAGVIVAAGHTNALYATMRQALEHGLTGFTHLFNAMSPLTSREPGAVGAALESPDAW
Sbjct: 181 RLADAGVIVAAGHTNALYATMRQALEHGLTGFTHLFNAMSPLTSREPGAVGAALESPDAW 240

Query: 241 CGIIVDGRHVDPVVLKIALRTRALDRFMLVTDAMPTVGLPDKRFNLQGRDIRVVDGVCVD 300
           CGIIVDGRHVDPVVLKIALRTRALDRFMLVTDAMPTVGLPDKRFNLQGRDIRVVDGVCVD
Sbjct: 241 CGIIVDGRHVDPVVLKIALRTRALDRFMLVTDAMPTVGLPDKRFNLQGRDIRVVDGVCVD 300

Query: 301 DHGTLAGSDLDMIGAVRNAIDLLDLSLDDAVMMASHAPASFLGLGHGRGLIAPGYAADLC 360
           DHGTLAGSDLDMIGAVRNAIDLLDLSLDDAVMMASHAPASFLGLGHGRGLIAPGYAADLC
Sbjct: 301 DHGTLAGSDLDMIGAVRNAIDLLDLSLDDAVMMASHAPASFLGLGHGRGLIAPGYAADLC 360

Query: 361 LLNDRLEVAATWIDGQEG 378
           LLNDRLEVAATWIDGQEG
Sbjct: 361 LLNDRLEVAATWIDGQEG 378


Lambda     K      H
   0.321    0.140    0.410 

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: 738
Number of extensions: 19
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: 378
Length of database: 378
Length adjustment: 30
Effective length of query: 348
Effective length of database: 348
Effective search space:   121104
Effective search space used:   121104
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate CCNA_00452 CCNA_00452 (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.12148.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.5e-104  333.8   0.0   7.3e-104  333.6   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_00452  CCNA_00452 N-acetylglucosamine-6


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_00452  CCNA_00452 N-acetylglucosamine-6-phosphate deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.6   0.0  7.3e-104  7.3e-104       6     379 ..       4     375 ..       1     376 [. 0.97

  Alignments for each domain:
  == domain 1  score: 333.6 bits;  conditional E-value: 7.3e-104
                             TIGR00221   6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtndasv.e 77 
                                           +l++ ++lte  v++ +av+++d++i +v+  a+ + + k +dlkg  l pG+iD q+nG+gGv +nda + e
  lcl|FitnessBrowser__Caulo:CCNA_00452   4 ALINGRVLTESGVVEGKAVLVKDGLILDVIEAAQTPSDAKPRDLKGGLLVPGFIDTQVNGGGGVLFNDAPTvE 76 
                                           799*****************************************************************7666* PP

                             TIGR00221  78 tleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGahpkeyire 150
                                           t+  +  a  + G+t+fLptli+ +   + +a++++ e++a+     +LGlh+eGPfl++++kG+h     r 
  lcl|FitnessBrowser__Caulo:CCNA_00452  77 TIATIGAAHRRFGTTGFLPTLISDDLRVVDQAMRATEEAIARGVP-GVLGLHIEGPFLNPKRKGIHDAGKFRV 148
                                           ******************************************988.8************************** PP

                             TIGR00221 151 pdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafkaGitfathlynam 223
                                           +d e l  +l+      t vtlap e++t ++i++l++ag+iv aGhtna y+++++a + G t  thl+nam
  lcl|FitnessBrowser__Caulo:CCNA_00452 149 IDDEAL-ALLTSLKRGKTLVTLAP-ERTTPQIIRRLADAGVIVAAGHTNALYATMRQALEHGLTGFTHLFNAM 219
                                           **9995.556665566799*****.89999******************************************* PP

                             TIGR00221 224 skldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaaagaklekfifaGkevy 296
                                           s+l+ Repg++Ga+L++ d  ++ii+DG h++p  +++a + +   +++lvtD++ + g+++++f  +G+++ 
  lcl|FitnessBrowser__Caulo:CCNA_00452 220 SPLTSREPGAVGAALESPDAWCGIIVDGRHVDPVVLKIALRTRALDRFMLVTDAMPTVGLPDKRFNLQGRDIR 292
                                           ************************************************************************* PP

                             TIGR00221 297 iredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnparalgiddrlGsvakGkdanLavltkd 369
                                           + ++ ++d++gtlaGs l mi +v+n+++  ++sl+d+v ++s  pa  lg+ + +G++a G+ a+L +l+  
  lcl|FitnessBrowser__Caulo:CCNA_00452 293 VVDGVCVDDHGTLAGSDLDMIGAVRNAIDLLDLSLDDAVMMASHAPASFLGLGHGRGLIAPGYAADLCLLNDR 365
                                           ************************************************************************* PP

                             TIGR00221 370 feviltiveg 379
                                            ev  t ++g
  lcl|FitnessBrowser__Caulo:CCNA_00452 366 LEVAATWIDG 375
                                           ******9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (378 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: 12.09
//
[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