GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG in Klebsiella michiganensis M5al

Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate BWI76_RS27535 BWI76_RS27535 PTS transporter subunit IIBC

Query= BRENDA::P69786
         (477 letters)



>FitnessBrowser__Koxy:BWI76_RS27535
          Length = 519

 Score =  226 bits (576), Expect = 1e-63
 Identities = 162/512 (31%), Positives = 256/512 (50%), Gaps = 51/512 (9%)

Query: 8   NLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVS-----HVMAEAGGS----VFAN 58
           N+QK  ++++  V  LP+ G++L + S   +  P ++S     H + +  G     +F N
Sbjct: 11  NMQKFSRAMIGAVLFLPVIGLILALSSVLTN--PTLISETSFLHQLGQLLGDTFWPLFGN 68

Query: 59  MPLIFAIGVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKH------ 112
           + L+F +G++ G   +         V   IM            H  AE+I  ++      
Sbjct: 69  LGLLFCVGISYGLAKDKKTEVALVSVMCFIMFLGANHSWLEHTHGLAEKINGEYYGTGQT 128

Query: 113 ------LADTGVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGV 166
                 + D GV  GII G   A++ N+   I+LP  L  + G +   +      IF  +
Sbjct: 129 QLLGFVVVDMGVFLGIILGCTIAWVHNKVSTIELPGALSMYGGAKLTLVAMTPVVIFYAI 188

Query: 167 VLSFIWPPIGSAIQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQM-QIGEY 225
             ++ WP +   I   + +         F +YGF E+ L+P GLHH    PFQ+ QIG  
Sbjct: 189 AFTWFWPFMTHGIAALTGFMKNAGVAGVF-VYGFFEKFLIPTGLHHFVWSPFQLTQIGGT 247

Query: 226 TNAAGQVFHGDIPRYMA----GDPT-----AGKLSGGFLFKMYGLPAAAIAIWHSAKPEN 276
            +  GQV  G    ++A     D T     A + S   +  ++GL  A++A +H+AKPE 
Sbjct: 248 LSVDGQVVSGTQAIFLAYMRHPDLTPVMNEALRFSQQGMTTIFGLAGASLAFYHTAKPEK 307

Query: 277 RAKVGGIMISAALTSFLTGITEPIEFSFMFVAPILYIIHAILAGLAFPICILLGMRD-GT 335
           +     I++ A +TS LTGITEPIEF+F+FV+P+L++IHA L   +  IC +  +R  G 
Sbjct: 308 KMMAKAILLPAIITSMLTGITEPIEFTFLFVSPLLWVIHATLTAASQAICDIFTVRPWGA 367

Query: 336 SFSHGLIDFIV----LSGNSSKLWLFPIVGIGYAIVYYTIFRVLIKALDLKTPGRED--- 388
           S   GLI+F++    L  + ++   + ++GIG   VYY IFR L+  L+LKTPGRED   
Sbjct: 368 S---GLIEFLIYNLPLPVSLTRWPGYVLIGIGQFAVYYVIFRTLVVKLNLKTPGREDDEN 424

Query: 389 ------ATEDAKATGTSEMAPALVAAFGGKENITNLDACITRLRVSVADVSKVDQAGLKK 442
                 A    K      +   ++   GGKENI ++D C TRLRV++ ++  VD   LK 
Sbjct: 425 VKLYSKADYRKKMGEPQSVTNEIINGLGGKENIISVDNCFTRLRVAIHNMDLVDDTILKS 484

Query: 443 LGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYI 474
            GA GVV   + VQ I+G K   +++ +D ++
Sbjct: 485 TGANGVVRNRNEVQVIYGVKVGQVRSRVDSWL 516


Lambda     K      H
   0.325    0.140    0.422 

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: 667
Number of extensions: 45
Number of successful extensions: 7
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: 477
Length of database: 519
Length adjustment: 34
Effective length of query: 443
Effective length of database: 485
Effective search space:   214855
Effective search space used:   214855
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: 40 (21.6 bits)
S2: 52 (24.6 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