GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_1647
          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 (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