GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsC in Klebsiella michiganensis M5al

Align IIC' aka PtsC2, component of N-Acetylglucosamine (NAG) porter (PtsBC1C2)(also may facilitate xylose transport) (characterized)
to candidate BWI76_RS11130 BWI76_RS11130 PTS glucose transporter subunit IIBC

Query= TCDB::Q8GBT6
         (403 letters)



>FitnessBrowser__Koxy:BWI76_RS11130
          Length = 477

 Score =  336 bits (862), Expect = 8e-97
 Identities = 177/398 (44%), Positives = 249/398 (62%), Gaps = 19/398 (4%)

Query: 2   AVLQRIGRSLMLPVAVLPAAALLVRLGNADMLGRPEFPAFVTKIAGFMAAGGNAILDNMA 61
           A LQ++G+SLMLPV+VLP A +L+ +G+A+       PA V+ +   MA  G ++  NM 
Sbjct: 7   ANLQKVGKSLMLPVSVLPIAGILLGVGSANFSW---LPAVVSHV---MAEAGGSVFANMP 60

Query: 62  LLFAVGIAIGFAKKSDGSTALAAVVGYLVFKNVLATFTDKNLPQVAKAVDGKVVMVDAPV 121
           L+FA+G+A+GF   +DG +ALA+VV Y +    ++      L   A+ +  K +      
Sbjct: 61  LIFAIGVALGFTN-NDGVSALASVVAYGIMVKTMSVVAPLVLHLPAEEIAAKHL-----A 114

Query: 122 DAKVLGGVVMGLVVALLYQRFYRTKLPDWAGFFGGRRLVPILSAFAGLVIGIVFGYIWPV 181
           D  VLGG++ G + A ++ RFYR KLP++ GFF G+R VPI+S  A +  G++  +IWP 
Sbjct: 115 DTGVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVILSFIWPP 174

Query: 182 LGTGLHNFGEWLVGSGAVGA-GIFGVANRALIPIGMHHLLNSFPWFQAGEYEGKSG---- 236
           +GT +  F +W      V A GI+G   R L+P G+HH+ N     Q GEY   +G    
Sbjct: 175 IGTAIQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFH 234

Query: 237 -DIARFLAGDPTAGQFMTGFFPIMMFALPAACLAIVHCARPERRKVVGGMMFSLALTSFV 295
            DI R++AGDPTAG+   GF    M+ LPAA +AI H A+PE R  VGG+M S ALTSF+
Sbjct: 235 GDIPRYMAGDPTAGKLSGGFL-FKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFL 293

Query: 296 TGVTEPIEFTFMFIAPVLYAIHAVLTGVSMALTWALGMKDGFGFSAGAVDFFLNLGIASN 355
           TG+TEPIEF+FMF+AP+LY IHA+L G++  +   LGM+DG  FS G +DF +  G +S 
Sbjct: 294 TGITEPIEFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSK 353

Query: 356 PWGLALVGVCFAALYYVVFRFAITKFNLPTPGRESDEE 393
            W   +VG+C+A +YYVVFR  I   +L TPGRE   E
Sbjct: 354 LWLFPIVGICYAIVYYVVFRVLIKALDLKTPGREDATE 391


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: 605
Number of extensions: 37
Number of successful extensions: 8
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: 477
Length adjustment: 32
Effective length of query: 371
Effective length of database: 445
Effective search space:   165095
Effective search space used:   165095
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.

Links

Downloads

Related tools

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