GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruA in Klebsiella michiganensis M5al

Align PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 (characterized)
to candidate BWI76_RS27570 BWI76_RS27570 phosphotransferase system, fructose-specific IIC component

Query= SwissProt::P23355
         (580 letters)



>FitnessBrowser__Koxy:BWI76_RS27570
          Length = 363

 Score =  299 bits (766), Expect = 1e-85
 Identities = 157/333 (47%), Positives = 212/333 (63%), Gaps = 6/333 (1%)

Query: 245 KHLMTGVSFMLPFVTAGGLLIALAFALGGIYAGDDAHQGTLAWSLFQIGAKAGFTLMVPA 304
           KHL+TG+S+M+P + A G+ IAL   LGG   G+    GT+ W L QIG   G  L+VP 
Sbjct: 14  KHLLTGISWMIPLIVAAGICIALGQVLGGTNVGEKT--GTIPWMLNQIGGW-GMGLIVPL 70

Query: 305 LAGYIAYSIADRPGIAPGMIGGLVAANLNAGFLGGIIAGFIAGYGVAALNRYIKLPRNLE 364
           +   IAYSIADRPG APG+I G V   ++ GF+GG++ GF+ GY V AL  YI+LP++++
Sbjct: 71  ICAAIAYSIADRPGFAPGLIVGFVCGQIHTGFIGGMLGGFLVGYTVLALKHYIRLPKSMQ 130

Query: 365 GLKPVLILPVLGTLLVGLAMMYVFGQPVADLLAWLTAWLRGMQGSSALLLGLLLGGMMAF 424
           GL P+++LPVL T++ GL MM + G+P+A L   L   L  MQG S  LLG +LG M  F
Sbjct: 131 GLMPIMVLPVLSTIISGLLMMTLIGKPIAWLQDALIHLLESMQGGSRFLLGAILGAMATF 190

Query: 425 DMGGPVNKAAYAFSTGLIASQVYTPMAAAMVAGMTPPLGIALATWVFRNRFTVEERGSAT 484
           D GGPVNK    F+ GL+ S VY P A   V  + PP GI L+  + R+++T  ER +  
Sbjct: 191 DFGGPVNKTMSLFADGLLVSGVYGPEAVKFVGSIIPPFGITLSFLLTRHKYTRAEREALK 250

Query: 485 AAGVLGLAFVTEGAIPYAARDPLRTIPALVIGSAVAGAISMTAGAELKAPHGGIFVLLIP 544
           AA  +G+  +TEG IP AARD LR + + V+ SAVAG + MT G E   PHGG+FV+ + 
Sbjct: 251 AAFPMGICMITEGVIPIAARDLLRVVGSCVVASAVAGGLIMTWGVESPVPHGGMFVVPL- 309

Query: 545 NAVTHLLNYVLALVVGVVVTAVALRLLKKPVAD 577
              TH L + L+L +G V+  V L L KKPV +
Sbjct: 310 --FTHPLLFCLSLAIGTVICGVMLSLWKKPVTE 340


Lambda     K      H
   0.320    0.135    0.386 

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: 468
Number of extensions: 22
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: 580
Length of database: 363
Length adjustment: 33
Effective length of query: 547
Effective length of database: 330
Effective search space:   180510
Effective search space used:   180510
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 (21.8 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