GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Lactobacillus shenzhenensis LY-73

Align glucosamine-6-phosphate deaminase subunit (EC 3.5.99.6) (characterized)
to candidate WP_022529337.1 L248_RS06470 glucosamine-6-phosphate deaminase

Query= metacyc::MONOMER-13104
         (235 letters)



>NCBI__GCF_000469325.1:WP_022529337.1
          Length = 235

 Score =  272 bits (696), Expect = 4e-78
 Identities = 137/233 (58%), Positives = 164/233 (70%)

Query: 1   MKIIQVENQVEGGKVALELLKEKLAQGAKTLGLATGSSPEEFYKQIVESDLDFSEMTSVN 60
           M II V++  EGG+ A  + KE LA  AK  GLATGS+P   Y  +  SDLDFS+  S+N
Sbjct: 1   MNIITVKDAQEGGQKAFNIFKEALAADAKVFGLATGSTPITLYNALTASDLDFSQKISIN 60

Query: 61  LDEYVGLQEEDPQSYRYFMNQHLFNQKPFKASFLPNGAAKDLEAEVARYNQLLTEHPADL 120
           LDEYVGL  ++PQSY YFM QHLFNQKPFK S++PNG AKD +AE  RY+ ++  +P DL
Sbjct: 61  LDEYVGLAPDNPQSYHYFMQQHLFNQKPFKTSYVPNGLAKDADAETQRYDDIIAANPIDL 120

Query: 121 QILGIGTNGHIGFNEPGTSFDSQTHLVDLTPSTIQSNARFFDKMEDVPTQAISMGIGNIL 180
           QILGIG NGHIGFNEPG+  + +TH V LT STI +NARFFD  EDVP  A SMGIG+I+
Sbjct: 121 QILGIGRNGHIGFNEPGSPLNGKTHKVPLTQSTIDANARFFDNEEDVPRFAYSMGIGSIM 180

Query: 181 NAKSIILFAYGSAKAKAIAGTVEGEVTEELPGSALQKHPDVVIIADKEALSLL 233
            AK I+L AYG  KA AI   VEG VT  +P SALQ H  V +I D+ A S L
Sbjct: 181 TAKHILLMAYGENKADAIQKMVEGPVTNHVPASALQNHNHVTVIVDEAAASKL 233


Lambda     K      H
   0.313    0.132    0.362 

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: 182
Number of extensions: 3
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: 235
Length of database: 235
Length adjustment: 23
Effective length of query: 212
Effective length of database: 212
Effective search space:    44944
Effective search space used:    44944
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 46 (22.3 bits)

Align candidate WP_022529337.1 L248_RS06470 (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.2797963.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.3e-78  248.2   0.1    4.7e-78  248.1   0.1    1.0  1  NCBI__GCF_000469325.1:WP_022529337.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000469325.1:WP_022529337.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.1   0.1   4.7e-78   4.7e-78       1     247 [.       1     233 [.       1     235 [] 0.93

  Alignments for each domain:
  == domain 1  score: 248.1 bits;  conditional E-value: 4.7e-78
                             TIGR00502   1 mklliletyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnlde 73 
                                           m +++++ ++e ++ a +i +e + +   da+   v+GlatG+tP++ly++l     a +++f++ + +nlde
  NCBI__GCF_000469325.1:WP_022529337.1   1 MNIITVKDAQEGGQKAFNIFKEALAA---DAK---VFGLATGSTPITLYNALT----ASDLDFSQKISINLDE 63 
                                           77888888888888888888888777...655...9**************995....789************* PP

                             TIGR00502  74 yvglseehPesyhsfmyenffqhidikpeninilnGnaddleaecrryeekikslGkidlfllGiGadGhiaf 146
                                           yvgl +++P+syh+fm++++f+    k    +++nG a+d +ae +ry++ i  +  idl++lGiG++Ghi+f
  NCBI__GCF_000469325.1:WP_022529337.1  64 YVGLAPDNPQSYHYFMQQHLFNQKPFK--TSYVPNGLAKDADAETQRYDDIIA-ANPIDLQILGIGRNGHIGF 133
                                           *********************987665..5689****************9886.679**************** PP

                             TIGR00502 147 nePgsslesrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegs 219
                                           nePgs l+ +t+ + lt++ti an+rff++  + vP+ a ++Gi+ i+ +k++ll++ G++ka+a++k+veg+
  NCBI__GCF_000469325.1:WP_022529337.1 134 NEPGSPLNGKTHKVPLTQSTIDANARFFDN-EEDVPRFAYSMGIGSIMTAKHILLMAYGENKADAIQKMVEGP 205
                                           *****************************6.578*************************************** PP

                             TIGR00502 220 vnedvtisalqlhkkvivvadeeaaqel 247
                                           v++ v++salq h++v+v++de+aa++l
  NCBI__GCF_000469325.1:WP_022529337.1 206 VTNHVPASALQNHNHVTVIVDEAAASKL 233
                                           *************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (259 nodes)
Target sequences:                          1  (235 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: 19.93
//
[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