GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEcb in Paraburkholderia bryophila 376MFSha3.1

Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate H281DRAFT_01853 H281DRAFT_01853 PTS system D-glucose-specific IIB component, Glc family /PTS system D-glucose-specific IIC component, Glc family

Query= reanno::pseudo3_N2E3:AO353_04465
         (571 letters)



>FitnessBrowser__Burk376:H281DRAFT_01853
          Length = 596

 Score =  426 bits (1096), Expect = e-123
 Identities = 253/591 (42%), Positives = 347/591 (58%), Gaps = 45/591 (7%)

Query: 9   LQRLGRALMLPIAILPIAGLLLRLGDTDL------LNIAIIHDAGQVIFANLALIFAIGI 62
           LQ++G++LMLP+A+LP+AGLLL LG TD       + +A++ +AG VIFANL LIFAIG+
Sbjct: 9   LQKVGKSLMLPVAVLPVAGLLLGLGATDFHGYVPAIVLALMKNAGDVIFANLPLIFAIGV 68

Query: 63  AVGFARDNNGTAGLAGAIGYLVMVSTLKVLDA-------------SINMGMLAGIISGLM 109
           A+GF  +N+G +G+A  IGYLVM +TL V+               SI  G+  GI++G +
Sbjct: 69  ALGFT-ENDGVSGIAATIGYLVMTATLGVIAKVEGIEPDMIMGIPSIQTGVFGGILAGGL 127

Query: 110 AGALYNRFKDIKLPEYLAFFGGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQLLL 169
           A  ++NR+  I LP YL FF G+RFVPI T   ++ LG I  ++WPPI   I +F Q   
Sbjct: 128 AAWMFNRYYRIALPAYLGFFAGKRFVPIVTAIGSIVLGAILSVVWPPIGSAIKAFSQWAA 187

Query: 170 ESGS-IGAFVFGVFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDPK 228
            S     A V+G   RLLI  GLHHI N   +F  GSF DPTTG +V GD+ R+FAGD  
Sbjct: 188 VSDPRTAATVYGFVERLLIPFGLHHIWNVPFFFEAGSFLDPTTGKVVHGDITRFFAGDRT 247

Query: 229 GGQFMTGMFPMMIFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFM 288
            G  + G F   +FGLPAA +A++  A PE +  +GG+ +S ALTSFLTG+TEPIEFAF+
Sbjct: 248 AG-ILAGAFLFKMFGLPAAAIAIWHCAKPENKVAVGGMMVSAALTSFLTGITEPIEFAFL 306

Query: 289 FLAPLLYLLHVLLTGMAMAITNALNIHLGFTFSGGAIDMA---LGWGKSTNGWLVFPVGL 345
           F+AP+LYL+H  L   A  + N L + +GFTFS G ID     L   KST+ W VF +G 
Sbjct: 307 FVAPVLYLIHACLAASAQFVANTLGMRMGFTFSQGGIDFLMFNLIGNKSTHAWYVFILGP 366

Query: 346 AYAVIYYVVFDFCIRRFNLKTPGREGVVVGEKVVLSE--NQRAGAYIQALGGAENLITVG 403
            YAVIYY VF F I RF+LKTPGRE   V    V +     R+   + A GG  N+ ++ 
Sbjct: 367 IYAVIYYGVFRFVITRFDLKTPGREDDTVETAKVSTAGVGGRSRELVLAFGGRSNIDSLD 426

Query: 404 ACTTRLRLEMVDRNKASDSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPTA 463
           AC TRLR+ + +    ++ +LKALGA  VVR G G  +Q + GPL++++  ++ + + TA
Sbjct: 427 ACITRLRISVKNPALVNEGKLKALGAAGVVRVGNG--VQAIFGPLSENMKTDMHEYLKTA 484

Query: 464 GSALVAAV---VVTEEAPKAAPV-------------ETPEAQKWLNAVGGSDNVLQLDCV 507
           GS    A     V E A   A               +    +K   A+GG  N+ +LD +
Sbjct: 485 GSEADLAADGKAVAEAAASTATAIGSAQASAHSTTQQAERVEKIRAALGGVANIQKLDAL 544

Query: 508 AMTRIRLQLADGKALSECQLKDLGCQGVSALDGGVWHLLIGDKALSLSEAL 558
           A TR+R+ L D   L    LK  G      L  G + L++G  A +L+ A+
Sbjct: 545 AATRLRVGLRDASQLDTAALKAAGVPATQTLTNGEFDLIVGLDAPNLAGAM 595


Lambda     K      H
   0.325    0.142    0.421 

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: 890
Number of extensions: 37
Number of successful extensions: 10
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: 571
Length of database: 596
Length adjustment: 36
Effective length of query: 535
Effective length of database: 560
Effective search space:   299600
Effective search space used:   299600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 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