GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Gracilibacillus halophilus YIM-C55.5

Align Glucosamine-6-phosphate deaminase 1; GlcN6P deaminase 1; GNPDA 1; Glucosamine-6-phosphate isomerase 1; EC 3.5.99.6 (characterized)
to candidate WP_003465244.1 J416_RS03835 glucosamine-6-phosphate deaminase

Query= SwissProt::O35000
         (242 letters)



>NCBI__GCF_000359605.1:WP_003465244.1
          Length = 241

 Score =  261 bits (668), Expect = 7e-75
 Identities = 122/237 (51%), Positives = 164/237 (69%)

Query: 1   MKVMECQTYEELSQIAARITADTIKEKPDAVLGLATGGTPEGTYRQLIRLHQTENLSFQN 60
           M +++   Y+++S   A +  DT++      LGLATGGTP+GTY+QL++ HQ    S+Q+
Sbjct: 1   MNIIQATNYQDMSNQTAELIIDTVRNNDYVTLGLATGGTPKGTYQQLVKDHQLNQTSYQH 60

Query: 61  ITTVNLDEYAGLSSDDPNSYHFYMNDRFFQHIDSKPSRHFIPNGNADDLEAECRRYEQLV 120
           +TT NLDEY G+   DPNSY +YM+  FF  +D       IPNG A+DL  EC RYE+ +
Sbjct: 61  VTTFNLDEYVGMRPTDPNSYRYYMDQYFFDEVDIPEQNIHIPNGMAEDLPRECARYEKQI 120

Query: 121 DSLGDTDIQLLGIGRNGHIGFNEPGTSFKSRTHVVTLNEQTRQANARYFPSIDSVPKKAL 180
           D     D+Q+LGIG+NGHIGFNEPGT+F+S THVV L   TR+ANAR+F  +D VP  A+
Sbjct: 121 DDTNGIDLQILGIGKNGHIGFNEPGTAFESTTHVVELAHSTRKANARFFNHLDDVPTHAI 180

Query: 181 TMGIQTILSSKRILLLISGKSKAEAVRKLLEGNISEDFPASALHLHSDVTVLIDREA 237
           TMGI TI+ SK+ILLL SG+ KAEA+RKL+   + E  PAS L  HS+VT++ D+ A
Sbjct: 181 TMGIATIMKSKQILLLASGEDKAEAIRKLIHEEVDEHMPASVLRHHSNVTIIADQNA 237


Lambda     K      H
   0.316    0.133    0.375 

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: 208
Number of extensions: 9
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: 242
Length of database: 241
Length adjustment: 23
Effective length of query: 219
Effective length of database: 218
Effective search space:    47742
Effective search space used:    47742
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 bits)

Align candidate WP_003465244.1 J416_RS03835 (glucosamine-6-phosphate deaminase)
to HMM TIGR00502 (nagB: glucosamine-6-phosphate deaminase (EC 3.5.99.6))

# 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/TIGR00502.hmm
# target sequence database:        /tmp/gapView.3743950.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00502  [M=259]
Accession:   TIGR00502
Description: nagB: glucosamine-6-phosphate deaminase
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-96  307.2   1.5    4.6e-96  307.1   1.5    1.0  1  NCBI__GCF_000359605.1:WP_003465244.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000359605.1:WP_003465244.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.1   1.5   4.6e-96   4.6e-96       1     244 [.       1     238 [.       1     241 [] 0.98

  Alignments for each domain:
  == domain 1  score: 307.1 bits;  conditional E-value: 4.6e-96
                             TIGR00502   1 mklliletyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnlde 73 
                                           m ++++++y+++s+ +a+ i++++++  +d    + lGlatGgtP g+y+ql+++++ ++ s+++v+tfnlde
  NCBI__GCF_000359605.1:WP_003465244.1   1 MNIIQATNYQDMSNQTAELIIDTVRN--ND---YVTLGLATGGTPKGTYQQLVKDHQLNQTSYQHVTTFNLDE 68 
                                           89**********************99..33...468************************************* PP

                             TIGR00502  74 yvglseehPesyhsfmyenffqhidikpeninilnGnaddleaecrryeekikslGkidlfllGiGadGhiaf 146
                                           yvg+ + +P+sy ++m + ff+ +di ++ni+i+nG a+dl  ec rye++i++  +idl++lGiG++Ghi+f
  NCBI__GCF_000359605.1:WP_003465244.1  69 YVGMRPTDPNSYRYYMDQYFFDEVDIPEQNIHIPNGMAEDLPRECARYEKQIDDTNGIDLQILGIGKNGHIGF 141
                                           ************************************************************************* PP

                             TIGR00502 147 nePgsslesrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegs 219
                                           nePg+ +es t+v++l+++t+ an+rff+  ++ vP +a+t+Gi ti++sk++lll+sG++kaea++kl+ + 
  NCBI__GCF_000359605.1:WP_003465244.1 142 NEPGTAFESTTHVVELAHSTRKANARFFN-HLDDVPTHAITMGIATIMKSKQILLLASGEDKAEAIRKLIHEE 213
                                           ****************************9.9****************************************** PP

                             TIGR00502 220 vnedvtisalqlhkkvivvadeeaa 244
                                           v+e +++s+l+ h++v+++ad++a 
  NCBI__GCF_000359605.1:WP_003465244.1 214 VDEHMPASVLRHHSNVTIIADQNAL 238
                                           **********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (259 nodes)
Target sequences:                          1  (241 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: 15.99
//
[ok]

This GapMind analysis is from Sep 24 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:

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