GapMind for catabolism of small carbon sources

 

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

Align sucrose hydrolase (SuxB;XCC3359) (EC 3.2.1.-) (characterized)
to candidate H281DRAFT_06049 H281DRAFT_06049 trehalose synthase

Query= CAZy::AAM42629.1
         (637 letters)



>FitnessBrowser__Burk376:H281DRAFT_06049
          Length = 1153

 Score =  163 bits (412), Expect = 5e-44
 Identities = 124/447 (27%), Positives = 204/447 (45%), Gaps = 59/447 (13%)

Query: 69  QARPAALRHLDDSRAPGWFGQQDMLGYSAYVDRF-------AGTLRGVAERVPYLQELGV 121
           + +PA L   DD   P W+  +D + Y  ++  F        G   G+  ++ Y+ ELGV
Sbjct: 30  RGKPATLS--DD---PLWY--KDAIIYQVHIKSFFDANNDGVGDFPGLIAKLDYIAELGV 82

Query: 122 RYLHLLPFLRARAGDNDGGFAVSDYGQVEPALGSNDDLVALTARLRAANISLCADFVLNH 181
             + LLPF  +   D+  G+ ++DY  V P  G   D+        A  I +  + V+NH
Sbjct: 83  NAIWLLPFYPSPRRDD--GYDIADYRNVHPDYGQLSDVKRFIQEAHARGIRVITELVINH 140

Query: 182 TADDHAWAQAARAGDTRYLDYYHHFADRNAPDQYDTTLVQVFPQTAPGNFTWVDETRQWM 241
           T+D H W Q AR       ++ + +   +   +Y  T + +F  + P N+T       + 
Sbjct: 141 TSDQHPWFQRARRAKPGS-NHRNFYVWSDTDQKYQETRI-IFIDSEPSNWTHDPVAGAYY 198

Query: 242 WTTFYPYQWDLNWSNPAVFGEMALAMLELANLGVEAFRLDSTAYLWKRPGTNCMNQPEAH 301
           W  FY +Q DLN+ NPAV  E+   M    ++G++  RLD+  YL +R GTN  N PE H
Sbjct: 199 WHRFYSHQPDLNFDNPAVLREVLQIMRFWLDMGIDGLRLDAVPYLVEREGTNNENLPETH 258

Query: 302 TILVALRAVADIVAPSVVMKAEAIVPMAELPPYFGSGVQRGHECHLAYHSTLMAAGWSAL 361
            IL  +RA  D   P+ ++ AEA     ++  YFG       ECH+A+H  LM   + ++
Sbjct: 259 AILKKIRATIDAEYPNRMLLAEANQWPEDVKEYFGD----EDECHMAFHFPLMPRIYMSI 314

Query: 362 ALQRGDILQDVIAHSPPLPPNCAWLSYVRCHDDIGWNVLQHEAAGTAAQPPFSLREVAQF 421
           A +    + D++  +P L     W  ++R HD++                  +L  V   
Sbjct: 315 ASEDRFPITDIMRQTPDLAETNQWAIFLRNHDEL------------------TLEMVTDS 356

Query: 422 YANAVPGSYARGESFQSSGDGVHGTNGMSAALVGVQAAHEHADAAAAARAVDRLVLLYAV 481
             + +  +YA              ++  +   +G++       A    R   R+ L+ ++
Sbjct: 357 ERDYLWNTYA--------------SDRRARLNLGIR----RRLAPLMERDRRRIELINSL 398

Query: 482 SLAMPGVPLIYMGDELALPNDTAYLDD 508
            L+MPG P+IY GDEL +  D  +L D
Sbjct: 399 LLSMPGTPVIYYGDELGM-GDNIHLGD 424


Lambda     K      H
   0.321    0.134    0.422 

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: 1772
Number of extensions: 100
Number of successful extensions: 5
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: 637
Length of database: 1153
Length adjustment: 42
Effective length of query: 595
Effective length of database: 1111
Effective search space:   661045
Effective search space used:   661045
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: 56 (26.2 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