GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-C in Klebsiella michiganensis M5al

Align Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized)
to candidate BWI76_RS27570 BWI76_RS27570 phosphotransferase system, fructose-specific IIC component

Query= TCDB::Q5V5X5
         (383 letters)



>FitnessBrowser__Koxy:BWI76_RS27570
          Length = 363

 Score =  254 bits (650), Expect = 2e-72
 Identities = 135/363 (37%), Positives = 206/363 (56%), Gaps = 19/363 (5%)

Query: 22  VKEDLMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGWFLAQIGVAGLTIMVPI 81
           +K+ L+TG+S+MIP +   GI +A+   +G T  V E TG+  W L QIG  G+ ++VP+
Sbjct: 12  IKKHLLTGISWMIPLIVAAGICIALGQVLGGTN-VGEKTGTIPWMLNQIGGWGMGLIVPL 70

Query: 82  LGGYIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGEAGAGYLGAIVAGLLAG 141
           +   IAY+IADRPG APG ++ ++                  G+   G++G ++ G L G
Sbjct: 71  ICAAIAYSIADRPGFAPGLIVGFVC-----------------GQIHTGFIGGMLGGFLVG 113

Query: 142 YVARFFKN-LDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVPVALANEGLTSFLQSMQ 200
           Y     K+ + +P+ +Q +MP++++PV +  +   +M+ ++G P+A   + L   L+SMQ
Sbjct: 114 YTVLALKHYIRLPKSMQGLMPIMVLPVLSTIISGLLMMTLIGKPIAWLQDALIHLLESMQ 173

Query: 201 GGQAIVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEIYAPMAAVMIGGMIPPIGLALS 260
           GG   ++G ILG M  FD GGPVNK   +FA GL+   +Y P A   +G +IPP G+ LS
Sbjct: 174 GGSRFLLGAILGAMATFDFGGPVNKTMSLFADGLLVSGVYGPEAVKFVGSIIPPFGITLS 233

Query: 261 NFIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIPAIVAGSAVGGATSMAL 320
             +  HKY     E  K+   +G+  ITEG IP AA D LRV+ + V  SAV G   M  
Sbjct: 234 FLLTRHKYTRAEREALKAAFPMGICMITEGVIPIAARDLLRVVGSCVVASAVAGGLIMTW 293

Query: 321 GVTMPAPHGGIFVVLLSNQPLAFLGSILLGSLVTAVVATVIKPDFEDRVDTGAETSSTQP 380
           GV  P PHGG+FVV L   PL F  S+ +G+++  V+ ++ K    +R +   E +  + 
Sbjct: 294 GVESPVPHGGMFVVPLFTHPLLFCLSLAIGTVICGVMLSLWKKPVTERDEEFDELNDQKV 353

Query: 381 TDD 383
            DD
Sbjct: 354 KDD 356


Lambda     K      H
   0.322    0.139    0.399 

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: 521
Number of extensions: 35
Number of successful extensions: 4
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: 383
Length of database: 363
Length adjustment: 30
Effective length of query: 353
Effective length of database: 333
Effective search space:   117549
Effective search space used:   117549
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: 50 (23.9 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