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.2190250.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 16.32
//
[ok]

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

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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