GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagEIIA in Sphingomonas koreensis DSMZ 15582

Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate Ga0059261_1647 Ga0059261_1647 PTS system, N-acetylglucosamine-specific IIBC component

Query= SwissProt::P39816
         (631 letters)



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

 Score =  366 bits (940), Expect = e-105
 Identities = 211/500 (42%), Positives = 293/500 (58%), Gaps = 32/500 (6%)

Query: 3   KKAFQILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNIPIIKDAGGVVFDNLPLIFAVGV 62
           +K  + LQ LGRALM P+AVLP AGLLLR G  DLL+I  +  AG  +F NL ++FA+GV
Sbjct: 2   RKILETLQPLGRALMLPIAVLPVAGLLLRIGQPDLLDIAFVSAAGTAIFGNLGILFAIGV 61

Query: 63  AIGLA-GGEGVAGLAAVIGYLILTVTLDNMGKLLGLQPPYEGAEHLID------------ 109
           A+G A  G G A LA V  YL+ T      G    L  P E    L D            
Sbjct: 62  AVGFARDGNGAAALAGVTCYLVSTT-----GAQTFLIAPPEVVAGLPDAAAKVVAQAWAT 116

Query: 110 -----MGVFGGIIIGLLAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSSLVIGVIFSF 164
                + V  GII GL+    Y RF++I L   L FF G+RFVPI   ++ L++  +  +
Sbjct: 117 GQIDRLEVPIGIISGLIGGKFYNRFATIALPEYLAFFGGRRFVPIAAGIAGLLLAGVLGY 176

Query: 165 VWPLIQNGINAASSLIADST-VGLFFYATIYRLLIPFGLHHIFYTPFYFMMGEYTDPSTG 223
            +  I + ++AAS  + +S   G+F Y  + RLL+  GLHH+     +F++G++      
Sbjct: 177 GYAHISSALDAASHAVVESGGAGMFVYGVLNRLLLVTGLHHLLNNVAWFLVGDF------ 230

Query: 224 NTVTGDLTRFFAGDPTAGRFMMGDFPYMIFCLPAVALAIIHTARPEKKKMISGVMISAAL 283
              TGDL RFFAGDP AG FM G FP M+F LPA  LA+ H ARPE++K + G++ S A 
Sbjct: 231 GGATGDLGRFFAGDPNAGAFMSGFFPVMMFGLPAACLAMYHEARPERRKAVGGMLFSLAF 290

Query: 284 TSMLTGITEPVEFSFLFVAPVLYLINSILAGVIFVVCDLFHVRHGYTFSGGGIDYVLNYG 343
           TS LTG+TEP+EF+F+F+APVLY I+++L GV   + D+  ++ G+ FS G  DYVLN+ 
Sbjct: 291 TSFLTGVTEPIEFTFMFLAPVLYAIHAVLTGVAMTLMDMLGIKLGFGFSAGLFDYVLNFK 350

Query: 344 LSTNGWVVIPVGIVFAFIYYYLFRFAILKWNLKTPGRETDEDGQNEEKAPVAKDQLAFHV 403
           LST  W+++PVG  +A IYY LFRF I K +L TPGRE  E      +     ++ A  V
Sbjct: 351 LSTRPWMLLPVGAAYAVIYYTLFRFFIRKLDLATPGREKGEAVAAAGETAAGNERGAAFV 410

Query: 404 LQALGGQQNIANLDACITRLRVTVHQPSQVCKDELKRLGAVGVLEVN-NNFQAIFGTKSD 462
            +ALGG  N+ ++DAC TRLR+ V   S V    L  LGA G++  + N  Q + G  +D
Sbjct: 411 -KALGGAANLTSVDACTTRLRLIVADQSAVDDAALNALGARGIIRPSANATQVVLGPIAD 469

Query: 463 ALKDDIKTIMAGGVPATAAA 482
            + ++I+  + GG  A +AA
Sbjct: 470 LVAEEIRGAIGGGAAAVSAA 489


Lambda     K      H
   0.324    0.142    0.421 

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: 915
Number of extensions: 58
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 631
Length of database: 560
Length adjustment: 37
Effective length of query: 594
Effective length of database: 523
Effective search space:   310662
Effective search space used:   310662
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 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