GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ptsC in Sphingomonas koreensis DSMZ 15582

Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate Ga0059261_1647 Ga0059261_1647 PTS system, N-acetylglucosamine-specific IIBC component

Query= TCDB::Q8GBT6
         (403 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1647 Ga0059261_1647 PTS system,
           N-acetylglucosamine-specific IIBC component
          Length = 560

 Score =  381 bits (979), Expect = e-110
 Identities = 200/407 (49%), Positives = 260/407 (63%), Gaps = 29/407 (7%)

Query: 1   MAVLQRIGRSLMLPVAVLPAAALLVRLGNADMLGRPEFPAFVTKIAGFMAAGGNAILDNM 60
           +  LQ +GR+LMLP+AVLP A LL+R+G  D+L              F++A G AI  N+
Sbjct: 5   LETLQPLGRALMLPIAVLPVAGLLLRIGQPDLLD-----------IAFVSAAGTAIFGNL 53

Query: 61  ALLFAVGIAIGFAKKSDGSTALAAVVGYLVFKNVLATF------TDKNLPQVAKAV---- 110
            +LFA+G+A+GFA+  +G+ ALA V  YLV      TF          LP  A  V    
Sbjct: 54  GILFAIGVAVGFARDGNGAAALAGVTCYLVSTTGAQTFLIAPPEVVAGLPDAAAKVVAQA 113

Query: 111 --DGKVVMVDAPVDAKVLGGVVMGLVVALLYQRFYRTKLPDWAGFFGGRRLVPILSAFAG 168
              G++  ++ P+      G++ GL+    Y RF    LP++  FFGGRR VPI +  AG
Sbjct: 114 WATGQIDRLEVPI------GIISGLIGGKFYNRFATIALPEYLAFFGGRRFVPIAAGIAG 167

Query: 169 LVIGIVFGYIWPVLGTGLHNFGEWLVGSGAVGAGIFGVANRALIPIGMHHLLNSFPWFQA 228
           L++  V GY +  + + L      +V SG  G  ++GV NR L+  G+HHLLN+  WF  
Sbjct: 168 LLLAGVLGYGYAHISSALDAASHAVVESGGAGMFVYGVLNRLLLVTGLHHLLNNVAWFLV 227

Query: 229 GEYEGKSGDIARFLAGDPTAGQFMTGFFPIMMFALPAACLAIVHCARPERRKVVGGMMFS 288
           G++ G +GD+ RF AGDP AG FM+GFFP+MMF LPAACLA+ H ARPERRK VGGM+FS
Sbjct: 228 GDFGGATGDLGRFFAGDPNAGAFMSGFFPVMMFGLPAACLAMYHEARPERRKAVGGMLFS 287

Query: 289 LALTSFVTGVTEPIEFTFMFIAPVLYAIHAVLTGVSMALTWALGMKDGFGFSAGAVDFFL 348
           LA TSF+TGVTEPIEFTFMF+APVLYAIHAVLTGV+M L   LG+K GFGFSAG  D+ L
Sbjct: 288 LAFTSFLTGVTEPIEFTFMFLAPVLYAIHAVLTGVAMTLMDMLGIKLGFGFSAGLFDYVL 347

Query: 349 NLGIASNPWGLALVGVCFAALYYVVFRFAITKFNLPTPGRESDEELA 395
           N  +++ PW L  VG  +A +YY +FRF I K +L TPGRE  E +A
Sbjct: 348 NFKLSTRPWMLLPVGAAYAVIYYTLFRFFIRKLDLATPGREKGEAVA 394


Lambda     K      H
   0.328    0.143    0.441 

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: 728
Number of extensions: 39
Number of successful extensions: 3
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: 403
Length of database: 560
Length adjustment: 33
Effective length of query: 370
Effective length of database: 527
Effective search space:   194990
Effective search space used:   194990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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