GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacZ in Flavobacterium glycines Gm-149

Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate WP_066328323.1 BLR17_RS01490 glycosyl hydrolase

Query= SwissProt::E7CY69
         (757 letters)



>NCBI__GCF_900100165.1:WP_066328323.1
          Length = 744

 Score =  389 bits (999), Expect = e-112
 Identities = 231/699 (33%), Positives = 370/699 (52%), Gaps = 43/699 (6%)

Query: 9   VKDLTLEEKASLTSGGDAWHLQGVESKGIPSYMITDGPHGLRKSLASSAGETDLDDSVPA 68
           +  +TLEEK  +  G   +   GV   GIP   + DGP G+R+ ++  + +    D+  A
Sbjct: 53  ISKMTLEEKIGMLHGNSMFANGGVPRLGIPELKMADGPLGVREEISRDSWKPAGLDNDFA 112

Query: 69  TCFPPAAGLSSSWNPELIHKVGEAMAEECIQEKVAVILGPGVNIKRNPLGGRCFEYWSED 128
           T +P +  L+++WN  +    G ++ +E       ++L P +NI R PLGGR +EY +ED
Sbjct: 113 TYYPASGALAATWNTRMASLFGNSVGQELRARDKDMLLSPAINIVRTPLGGRTYEYMTED 172

Query: 129 PYLAGHEAIGIVEGVQSKGVGTSLKHFAANNQETDRLRVDARISPRALREIYFPAFEHIV 188
           P+L    A+ +V  +Q   V   +KHFAANNQET+R  VD +I  R LREIY P FE  +
Sbjct: 173 PFLNKKMAVPLVVSLQDNDVMACVKHFAANNQETNRDFVDVQIDERTLREIYLPTFEATI 232

Query: 189 KKAQPWTIMCSYNRINGVHSAQNHWLLTDVLRDEWGFDGIVMSDWGADHDRGASLNAGLN 248
           K+   +++M +YN+  G +  +N ++L  +LRDEWGF G+V+SDW A H    SL  GL+
Sbjct: 233 KEGNVYSVMGAYNKFRGEYLCENDYMLNTILRDEWGFKGVVVSDWAAVHSTVKSLQNGLD 292

Query: 249 LEMPPS------YTDDQIVYAVRDGLITPAQLDRMAQGMIDLVNKTRAAMSIDNYR--FD 300
           +EM         +  D+++ AV+ G ++  ++D+  + ++ ++ + +A    D  +    
Sbjct: 293 IEMGSKKPFNEYFLADKLIAAVKAGEVSEKEIDKHVKRILHVLFQVKAMDGKDRVKGSLA 352

Query: 301 VDAHDEVAHQAAIESIVMLKNDDAILPLNAGPVANPSATPQKIAVIGEFARTPRYQGGGS 360
            ++H + A++ A E++V+LKN++  LPL    +       + IAVIG  A      GG  
Sbjct: 353 TESHYQDAYEIASEAVVLLKNNNNALPLKLDGI-------KSIAVIGNNATKKNALGGFG 405

Query: 361 SHITPTKMTSFLDTLAER---GIKADFAPGF-------------------TLDLEPADPA 398
           + +   +  + L+ L  R    IK ++A G+                    + ++  D A
Sbjct: 406 AGVKTKREITPLEGLKNRLPASIKINYAEGYLERYEKKNKGNLGNITSKGPVTIDQLDDA 465

Query: 399 LESEAVETAKNADVVLMFLGLPEAVESEGFDRDTLDMPAKQIALLEQVAAANQNVVVVLS 458
              EA+E  KN+   ++F G     E+E  DR  L +P  Q  L+++V A N   +VV+ 
Sbjct: 466 KLQEALEAVKNSGAAIIFAGSNRDYETEASDRKDLKLPFGQEELIKKVLAINPKTIVVMI 525

Query: 459 NGSVITVAPWAKNAKGILESWLLGQSGGPALADVIFGQVSPSGKLAQSIPLDINDDPSML 518
            G+   +   +K    ++ SW  G  GG ALADV+ G+V+PSGKL  ++P  + D P+  
Sbjct: 526 AGAPFEMEEISKKTNALVWSWFNGSEGGNALADVLLGKVNPSGKLPWTMPKKLMDSPAHA 585

Query: 519 --NWPGEEGHVDYGEGVFAGYRYYDTYGKAVDYPFGYGLSYATFEITGVAVAKTGAN--- 573
             ++PG++  V+Y EG+  GYR++DT   +  YPFGYGLSY  F        K   N   
Sbjct: 586 TNSFPGDK-TVNYAEGILVGYRWFDTKKISPMYPFGYGLSYTNFTFGKAFSDKEIYNNDE 644

Query: 574 TATVTATVTNTSDVDAAETVQVYVVPGKADVARPKHELKGFTKAFLKAGESKTVAIDLDE 633
             T+   + NT  VD  E VQ+Y     + + R   ELKGFTK  +KAG ++ V I +  
Sbjct: 645 VITIAVDLKNTGKVDGKEVVQLYSSKTDSKIDRAAQELKGFTKILVKAGATQKVIIKVPV 704

Query: 634 RAFAYWSEKYNDWHVEAGEYAIEVGVSSRDIADTVAVAL 672
           +  AY+      W VE G+Y +++G SSRDI   + V +
Sbjct: 705 KELAYYDVANKKWTVEPGKYKLKLGNSSRDIKKEIDVII 743


Lambda     K      H
   0.315    0.132    0.393 

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: 1279
Number of extensions: 56
Number of successful extensions: 5
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: 757
Length of database: 744
Length adjustment: 40
Effective length of query: 717
Effective length of database: 704
Effective search space:   504768
Effective search space used:   504768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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