Alignments for a candidate for nagA in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagA in Azospirillum brasilense Sp245

Align N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25) (characterized)
to candidate AZOBR_RS11675 AZOBR_RS11675 N-acetylglucosamine 6-phosphate deacetylase

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



>FitnessBrowser__azobra:AZOBR_RS11675
          Length = 383

 Score =  365 bits (937), Expect = e-105
 Identities = 195/377 (51%), Positives = 243/377 (64%), Gaps = 4/377 (1%)

Query: 4   ALINGRVLTESGVVEGKAVLVKDGLILDVIEAAQTPSDAKPRDLKGGLLVPGFIDTQVNG 63
           AL+N  + T   V+ G A+L+    I  ++     P +A   DL GG+L PGFID QVNG
Sbjct: 3   ALVNATLHTGDSVLAGAALLIDGPAIAAIVAPEAIPPEAAVIDLGGGILAPGFIDLQVNG 62

Query: 64  GGGVLFNDAPTVETIATIGAAHRRFGTTGFLPTLISDDLRVVDQAMRATEEAIARGVPGV 123
           GGG LFND P + T+  I  AHRRFGTTG LPTLI+D       A+ A   A+A+G+PGV
Sbjct: 63  GGGALFNDTPDLPTLRRIAEAHRRFGTTGLLPTLITDSAEKRAVAVAAVRAALAQGMPGV 122

Query: 124 LGLHIEGPFLNPKRKGIHDAGKFRVIDDEALALLTSLKRGKTLVTLAPERTTPQIIRRLA 183
           LG+H+EGP + P+R+G+HDA      D + LALL  L     LVTLAPE   P+ IRRLA
Sbjct: 123 LGIHLEGPHIAPERRGVHDARFIAPPDADDLALLGGLSGLPALVTLAPEAVPPEPIRRLA 182

Query: 184 DAGVIVAAGHTNALYATMRQALEHGLTGFTHLFNAMSPLTSREPGAVGAALESPDAWCGI 243
            AG+ +AAGH+ A +A  +     G+TG THLFNAMSPL SREPG VGAALE    WCGI
Sbjct: 183 AAGLRIAAGHSTATWAQAKAGFAAGITGVTHLFNAMSPLGSREPGMVGAALEDDAVWCGI 242

Query: 244 IVDGRHVDPVVLKIALRTRALDRFMLVTDAMPTVGLPDK----RFNLQGRDIRVVDGVCV 299
           IVDG HV    +++A + +   R  LVTDAMP VG P+      F L G +IRV DG CV
Sbjct: 243 IVDGHHVHDASVRLAWKAKTPGRLFLVTDAMPPVGAPEDHPAGNFQLYGEEIRVEDGRCV 302

Query: 300 DDHGTLAGSDLDMIGAVRNAIDLLDLSLDDAVMMASHAPASFLGLGHGRGLIAPGYAADL 359
              GTLAGS LDM  AVRNA++ + + LD+A+ MAS  PA F+G+   RG I PG AADL
Sbjct: 303 TADGTLAGSALDMATAVRNAVERVGIPLDEALRMASAYPADFMGMAGRRGRIRPGLAADL 362

Query: 360 CLLNDRLEVAATWIDGQ 376
             L++RL V ATWI G+
Sbjct: 363 VHLDERLRVRATWISGK 379


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: 538
Number of extensions: 26
Number of successful extensions: 2
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: 383
Length adjustment: 30
Effective length of query: 348
Effective length of database: 353
Effective search space:   122844
Effective search space used:   122844
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 AZOBR_RS11675 AZOBR_RS11675 (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.14037.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-103  331.1   0.0   4.7e-103  331.0   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS11675  AZOBR_RS11675 N-acetylglucosamin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS11675  AZOBR_RS11675 N-acetylglucosamine 6-phosphate deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.0   0.0  4.7e-103  4.7e-103       6     380 .]       3     379 ..       1     379 [. 0.98

  Alignments for each domain:
  == domain 1  score: 331.0 bits;  conditional E-value: 4.7e-103
                                 TIGR00221   6 llkdkailtendvlddsavvindekikavvteaeleeeikeidlkgnvltpGliDvqlnGcgGvdtnda 74 
                                               +l + ++ t+  vl   a +i++  i a+v+ +  ++e   idl g +l+pG+iD+q+nG+gG+ +nd+
  lcl|FitnessBrowser__azobra:AZOBR_RS11675   3 ALVNATLHTGDSVLAGAALLIDGPAIAAIVAPEAIPPEAAVIDLGGGILAPGFIDLQVNGGGGALFNDT 71 
                                               7889999*************************************************************8 PP

                                 TIGR00221  75 sv.etleimsealaksGvtsfLptlitredeeikkavkvareylakeknakiLGlhleGPflslekkGa 142
                                                   tl  + ea  + G+t+ Lptlit + e+   av ++r++la+     +LG+hleGP++++e++G+
  lcl|FitnessBrowser__azobra:AZOBR_RS11675  72 PDlPTLRRIAEAHRRFGTTGLLPTLITDSAEKRAVAVAAVRAALAQGMP-GVLGIHLEGPHIAPERRGV 139
                                               766******************************************9988.9****************** PP

                                 TIGR00221 143 hpkeyirepdvellkkfldeagdvitkvtlapeekqtaelisklleagiivsaGhtnatyeelkeafka 211
                                               h   +i +pd++    +l   +++   vtlap e ++ e i++l+ ag+ + aGh+ at +++k++f a
  lcl|FitnessBrowser__azobra:AZOBR_RS11675 140 HDARFIAPPDADD-LALLGGLSGLPALVTLAP-EAVPPEPIRRLAAAGLRIAAGHSTATWAQAKAGFAA 206
                                               ***********98.6899999***********.99999******************************* PP

                                 TIGR00221 212 GitfathlynamskldhRepgviGavLdeddvvteiiaDGlhihpknirlakklkgdsklvlvtDslaa 280
                                               Git +thl+nams+l  Repg++Ga+L++d v ++ii+DG+h+h + +rla k+k   +l lvtD++ +
  lcl|FitnessBrowser__azobra:AZOBR_RS11675 207 GITGVTHLFNAMSPLGSREPGMVGAALEDDAVWCGIIVDGHHVHDASVRLAWKAKTPGRLFLVTDAMPP 275
                                               ********************************************************************* PP

                                 TIGR00221 281 agak....lekfifaGkevyiredtlldkngtlaGssltmiegvknlvefveislsdvvrisslnpara 345
                                                ga+     ++f+  G+e+ +++++++ ++gtlaGs+l m  +v+n+ve v+i+l++++r++s +pa  
  lcl|FitnessBrowser__azobra:AZOBR_RS11675 276 VGAPedhpAGNFQLYGEEIRVEDGRCVTADGTLAGSALDMATAVRNAVERVGIPLDEALRMASAYPADF 344
                                               9998777789*********************************************************** PP

                                 TIGR00221 346 lgiddrlGsvakGkdanLavltkdfeviltivegk 380
                                               +g+  r+G +  G  a+L+ l++  +v  t + gk
  lcl|FitnessBrowser__azobra:AZOBR_RS11675 345 MGMAGRRGRIRPGLAADLVHLDERLRVRATWISGK 379
                                               ******************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (383 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: 9.17
//
[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