GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malEIICBA in Klebsiella michiganensis M5al

Align Maltose/Maltotriose PTS transporter, MalT (Shelburne et al., 2008) 631aas (68% identical to 4.A.1.1.11 from S. mutans (characterized)
to candidate BWI76_RS08220 BWI76_RS08220 PTS N-acetyl glucosamine transporter subunit IIABC

Query= TCDB::Q48WG5
         (631 letters)



>FitnessBrowser__Koxy:BWI76_RS08220
          Length = 650

 Score =  267 bits (683), Expect = 9e-76
 Identities = 205/625 (32%), Positives = 308/625 (49%), Gaps = 65/625 (10%)

Query: 11  GVSSTMLADPE--AKITSLLGTQMIVKDYFTSVLESPALNTGVFVGIIAGFVGATAYNKY 68
           GV+S+   D    A +   +G  ++ K   T    +PA+N GV  GII G VG   YN++
Sbjct: 59  GVASSWSKDSAGAAALAGAVGYFVLTKAMVTI---NPAINMGVLAGIITGLVGGAVYNRW 115

Query: 69  YNYRKLPEVLTFFNGKRFVPFVVILRSIFVALILVVVWPVIQSGINSFGMWIASSQDSAP 128
               KLP+ L+FF GKRFVP       + +A I   VWP +Q+ I++ G WI      A 
Sbjct: 116 SGI-KLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQNAIHAGGEWIVG----AG 170

Query: 129 ILAPFLYGTLERLLLPFGLHHMLTIPMNYTALGGTYEVMTGAAAGTKVFGQDPLWLAWVT 188
            L   ++G + RLL+P GLH +L   + +  +G         AAG    G          
Sbjct: 171 ALGSGIFGFINRLLIPTGLHQVLNT-IAWFQIGEFTN-----AAGAVFHG---------- 214

Query: 189 DLVHLKGSDASAYSHLMDSVTPARFKVGQMIGATGTLMGVALAMYRNVDADKKHTYKMMF 248
           D+      D +A    M    P       M G    L G ALAMY     +++     M 
Sbjct: 215 DINRFYAGDGTA-GMFMSGFFPI-----MMFG----LPGAALAMYFAAPKERRPMVGGML 264

Query: 249 ISAAAAVFLTGVTEPLEYLFMFAAMPLYIVYALVQGASFAMADLVNLRV---HSFGNIE- 304
           +S A   FLTGVTEPLE+LFMF A  LY+++A++ G S  +A  + +      S G I+ 
Sbjct: 265 LSVAITAFLTGVTEPLEFLFMFLAPLLYLLHAILTGISLFVATALGIHAGFSFSAGAIDY 324

Query: 305 -LLTRTPMALKAGLGMDVINFVWVSVLFAVIMYFIADMMIKKMHLATAGRLGNYDADILG 363
            L+   P A K     +V   + + V+F VI + +   +I+  +L T GR    D  +  
Sbjct: 325 VLMYSLPAASK-----NVWMLIVMGVVFFVIYFLLFSAVIRMFNLKTPGREDKVDDVVTE 379

Query: 364 DRNTQTRP--TQVADSNSQVVQIVNLLGGAGNIDDVDACMTRLRVTVKDPAKVGAEDDWK 421
           + N+ T    TQ+A +       +  +GG  N+  +DAC+TRLR+TV D A V  +   K
Sbjct: 380 EANSNTEEGLTQLATN------YIAAVGGTDNLKAIDACITRLRLTVADSALVN-DAACK 432

Query: 422 KAGAIGLIQKGNG-VQAVYGPKADILKSDIQDLLDSGALIPEVNMSQLTSKPTPAKDFKH 480
           + GA G+++     +Q + G KA+ +  +++ ++  G +      S   S P  A+  K 
Sbjct: 433 RLGASGVVKLNKQTIQVIVGAKAESVGDEMKKVVARGPVAAAAAASH--SAPVAAQAVKP 490

Query: 481 VTEDVLSVADGMVLPITG-------VKDQVFAAKMMGDGFAVEPTHGNIYAPVAGLVTSV 533
                    + +V PITG       V D+ FA+K +GDG AV+PT   + AP AG V  +
Sbjct: 491 QAVANAKTVEALVSPITGDIVALEQVPDEAFASKAVGDGVAVKPTDKIVVAPAAGTVVKI 550

Query: 534 FPTKHAFGLLTDNGLEVLVHVGLDTVALNGVPFSVKVSEGQRVHAGDLLVVADLAAIKSA 593
           F T HAF L T+NG E++VH+G+DTVALNG  F   V EG  V AG+ ++  DL  + + 
Sbjct: 551 FNTNHAFCLETENGAEIVVHMGIDTVALNGQGFKRLVEEGAEVKAGEPILELDLEFLNAN 610

Query: 594 ERETIIVVAFTNTTEIQDVTLTSLG 618
            R  I  V  +N+ +   + + + G
Sbjct: 611 ARSMISPVVCSNSDDYSALVIQATG 635


Lambda     K      H
   0.322    0.137    0.396 

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: 894
Number of extensions: 42
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 631
Length of database: 650
Length adjustment: 38
Effective length of query: 593
Effective length of database: 612
Effective search space:   362916
Effective search space used:   362916
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: 54 (25.4 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