GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruA in Klebsiella michiganensis M5al

Align protein-Npi-phosphohistidine-D-fructose phosphotransferase (subunit 2/2) (EC 2.7.1.202) (characterized)
to candidate BWI76_RS24865 BWI76_RS24865 PTS family enzyme IIB'BC, fructose-specific

Query= BRENDA::Q8DWE7
         (466 letters)



>FitnessBrowser__Koxy:BWI76_RS24865
          Length = 470

 Score =  511 bits (1315), Expect = e-149
 Identities = 257/450 (57%), Positives = 331/450 (73%), Gaps = 2/450 (0%)

Query: 5   KLIAATGCPTGIAHTFMAQEALEQAAKEKGVSIKVETHGQVGVENELTPAEIAGAKAVII 64
           K+IA TGCPTGIAHTFMA+EAL+ AAK+  + IKVET+G  GVEN +TPA++     VII
Sbjct: 3   KIIAVTGCPTGIAHTFMAEEALKTAAKKLNIEIKVETNGASGVENAITPADLKDIYGVII 62

Query: 65  AADKDVQAERFAGKRVIEVSVADGIKKADQLIADALAGKGQIKGGTKIESAELSSDTEGE 124
           AADKDV AERF G  VIEV V + I     LI   ++G+   + G    S + +   E E
Sbjct: 63  AADKDVNAERFNGLPVIEVPVKEAIHHPADLINKFISGQAARRQGISA-SDDSTEKYERE 121

Query: 125 SFGRQVYRHLMNGVSHMLPFVVAGGVLVAISFLFGIYSFDPKSEQYNWFAALLKTDIGGV 184
           SFGRQVY+HLM+GVS+MLPFVVAGG+L+AISFL+GIYS DP S QYN  AA L   +G  
Sbjct: 122 SFGRQVYKHLMSGVSNMLPFVVAGGILIAISFLWGIYSADPNSPQYNVIAATLMK-VGQQ 180

Query: 185 AMGVMTPILAAYIAESIAKRPGFVAGFVGGMMAVNGGSGFLGGIIAGFAAGYIVLGLMKL 244
           A  +M PI  AYIA SI+ RPG VAGFVGG++A   G+GFLGGIIAGFAAGY +L +  +
Sbjct: 181 AFSIMVPIFTAYIAWSISGRPGMVAGFVGGLLANATGAGFLGGIIAGFAAGYFMLLIRNM 240

Query: 245 FEKLPKSLDGLKAIFLYPVFGVFLTGMVMAVVNSPMAWVNKSLMAWLGAFENANPLVLGV 304
              LP+  +GLK+IF+ P+ GV + G++M ++  P+A +N ++M WL + + ANP++LG+
Sbjct: 241 LNGLPRQYEGLKSIFIMPLVGVLVIGVMMVLLGQPVAAINNAMMNWLSSLQEANPILLGI 300

Query: 305 IVGCMCAFDMGGPVNKAAYVTGTALLAQGNTTFMAGVSAACIAPPLITFVATTAFRKYYD 364
           +VG MC+FD GGPVNKAAYVTGT LL QGN  FMAGVSAACI PPL+  +ATT F K + 
Sbjct: 301 VVGAMCSFDFGGPVNKAAYVTGTLLLGQGNYFFMAGVSAACITPPLVIALATTFFPKGFS 360

Query: 365 ENDRNAGLANLILGSTHITEGAIPFAAKDPLRMLPTFMLGSSIAAILTYMWKVKVPAPHG 424
           E +R AG+ N ILG THITEGAIPFAAKDPLR++P  M+ SSI+A+L+Y  +++VPAPHG
Sbjct: 361 EEERAAGMVNYILGCTHITEGAIPFAAKDPLRVIPMMMIASSISAVLSYSLQIQVPAPHG 420

Query: 425 GFLVLPVVTHAFLWVLAIAIGAIVAGIIMG 454
           GFL+LP+V+   +WVL I  G+    +++G
Sbjct: 421 GFLILPLVSKPLMWVLCILAGSACGAVMLG 450


Lambda     K      H
   0.322    0.138    0.406 

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: 637
Number of extensions: 21
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: 466
Length of database: 470
Length adjustment: 33
Effective length of query: 433
Effective length of database: 437
Effective search space:   189221
Effective search space used:   189221
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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 (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