GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Megamonas funiformis YIT 11815

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_008539730.1 HMPREF9454_RS10530 glucosamine-6-phosphate deaminase

Query= SwissProt::O35000
         (242 letters)



>NCBI__GCF_000245775.1:WP_008539730.1
          Length = 251

 Score =  260 bits (665), Expect = 2e-74
 Identities = 118/242 (48%), Positives = 179/242 (73%)

Query: 1   MKVMECQTYEELSQIAARITADTIKEKPDAVLGLATGGTPEGTYRQLIRLHQTENLSFQN 60
           M+++   +YEE+S++AARI A  +  KP++VLGLATG TPEG Y  L+++HQ+  L F  
Sbjct: 1   MRIIVTDSYEEMSKVAARIVAGQLYLKPNSVLGLATGSTPEGMYANLVKVHQSVGLDFSE 60

Query: 61  ITTVNLDEYAGLSSDDPNSYHFYMNDRFFQHIDSKPSRHFIPNGNADDLEAECRRYEQLV 120
           + + NLDEY GL  ++  SY+++M+   F H++ KP    IPNGN ++LE EC++Y++L+
Sbjct: 61  VISFNLDEYIGLDKENEQSYYYFMHKHLFDHVNIKPENIHIPNGNPENLEEECKKYDKLI 120

Query: 121 DSLGDTDIQLLGIGRNGHIGFNEPGTSFKSRTHVVTLNEQTRQANARYFPSIDSVPKKAL 180
           ++ G  D+Q+LGIG+N HIGFNEP   F++ TH V L+E+T +AN+R+F + + VPK A+
Sbjct: 121 EAKGGIDLQVLGIGQNAHIGFNEPDIKFEATTHKVKLDEETIKANSRFFENEEDVPKYAI 180

Query: 181 TMGIQTILSSKRILLLISGKSKAEAVRKLLEGNISEDFPASALHLHSDVTVLIDREAASL 240
           +MGI+TI+ +K+I+LL SGK+KAEA+ K + G++  D PAS L LH DV V++D++AASL
Sbjct: 181 SMGIKTIMLAKKIILLASGKNKAEAIYKAVYGSVRPDAPASILQLHQDVVVIVDKDAASL 240

Query: 241 RP 242
            P
Sbjct: 241 LP 242


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: 199
Number of extensions: 6
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: 242
Length of database: 251
Length adjustment: 24
Effective length of query: 218
Effective length of database: 227
Effective search space:    49486
Effective search space used:    49486
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_008539730.1 HMPREF9454_RS10530 (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.868781.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     3e-100  320.8   0.7   3.3e-100  320.7   0.7    1.0  1  NCBI__GCF_000245775.1:WP_008539730.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000245775.1:WP_008539730.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.7   0.7  3.3e-100  3.3e-100       1     255 [.       1     249 [.       1     251 [] 0.97

  Alignments for each domain:
  == domain 1  score: 320.7 bits;  conditional E-value: 3.3e-100
                             TIGR00502   1 mklliletyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnlde 73 
                                           m+++ ++ yee+sk+aari+a ++   kp+     vlGlatG+tP+g+y +l++++++  ++f++v+ fnlde
  NCBI__GCF_000245775.1:WP_008539730.1   1 MRIIVTDSYEEMSKVAARIVAGQLYL-KPN-S---VLGLATGSTPEGMYANLVKVHQSVGLDFSEVISFNLDE 68 
                                           9***********************97.999.5...9************************************* PP

                             TIGR00502  74 yvglseehPesyhsfmyenffqhidikpeninilnGnaddleaecrryeekikslGkidlfllGiGadGhiaf 146
                                           y+gl++e+ +sy++fm++++f+h++ikpeni+i+nGn ++le ec++y+++i+  G+idl++lGiG++ hi+f
  NCBI__GCF_000245775.1:WP_008539730.1  69 YIGLDKENEQSYYYFMHKHLFDHVNIKPENIHIPNGNPENLEEECKKYDKLIEAKGGIDLQVLGIGQNAHIGF 141
                                           ************************************************************************* PP

                             TIGR00502 147 nePgsslesrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegs 219
                                           neP  ++e  t+ ++l e+ti ansrffe+  + vPk+a+++Gikti+ +k+++ll+sGk+kaea+ k+v gs
  NCBI__GCF_000245775.1:WP_008539730.1 142 NEPDIKFEATTHKVKLDEETIKANSRFFEN-EEDVPKYAISMGIKTIMLAKKIILLASGKNKAEAIYKAVYGS 213
                                           *****************************6.578*************************************** PP

                             TIGR00502 220 vnedvtisalqlhkkvivvadeeaaqelkvktlkyf 255
                                           v  d ++s+lqlh++v+v++d++aa+ l+ k  k f
  NCBI__GCF_000245775.1:WP_008539730.1 214 VRPDAPASILQLHQDVVVIVDKDAASLLPEKDKKVF 249
                                           **************************9998766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (259 nodes)
Target sequences:                          1  (251 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: 14.46
//
[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