GapMind for catabolism of small carbon sources

 

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

Align β-galactosidase (A4-β-Gal) (EC 3.2.1.23) (characterized)
to candidate H281DRAFT_03229 H281DRAFT_03229 beta-galactosidase

Query= CAZy::BAA28362.1
         (645 letters)



>FitnessBrowser__Burk376:H281DRAFT_03229
          Length = 661

 Score =  692 bits (1786), Expect = 0.0
 Identities = 347/660 (52%), Positives = 438/660 (66%), Gaps = 23/660 (3%)

Query: 2   LGVCYYPEHWPKERWKEDARRMREAGLSHVRIGEFAWALLEPEPGRLEWGWLDEAIATLA 61
           LGVCYYPEHWP+  W++DARRM+  G+  VRI EFAW+ +EP PG  +W WLD AI  L 
Sbjct: 3   LGVCYYPEHWPESMWEDDARRMKALGIEQVRIAEFAWSRIEPTPGEYDWAWLDRAIEVLG 62

Query: 62  AEGLKVVLGTPTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRIVT 121
           A GL+VV+ TPTATPPKWL+DR+P+ILP+  +GR R FG RRHY FSSP Y   +++I T
Sbjct: 63  AAGLQVVMCTPTATPPKWLIDRHPDILPIGADGRPRAFGSRRHYDFSSPSYFSASQKICT 122

Query: 122 LLAERYGGLEAVAGFQTDNEYGCHDTVRCYCPRCQEAFRGWLEARYGTIEALNEAWGTAF 181
            +AERYG   AVA +QTDNE+GCH TV  Y P     FR WL+ARY TI+ LN AWGT F
Sbjct: 123 AIAERYGKHPAVAYWQTDNEFGCHHTVVSYSPAAVARFREWLKARYTTIDELNRAWGTVF 182

Query: 182 WSQRYRSFAEVELPHLTVAEPNPSHLLDYYRFASDQVRAFNRLQVEILRAHAPGKFVTHN 241
           WS  YRSF E++ P  TV E +PSH LDY RFASD+V  +NR+QVEI+RAH+PG+ V HN
Sbjct: 183 WSMEYRSFDEIDAPVATVTEAHPSHRLDYRRFASDEVARYNRMQVEIIRAHSPGRPVAHN 242

Query: 242 FMGFFTDLDAFALAQDLDFASWDSYPLGFTDLMPLPPEEKLRYARTGHPDVAAFHHDLYR 301
           FM  FT+ D + +A DLD A+WDSYPLG  +     P+ K R+ R+GHPD A+F+HD+YR
Sbjct: 243 FMQLFTEFDHYKVAADLDVAAWDSYPLGALEEQWFAPDVKARWLRSGHPDFASFNHDVYR 302

Query: 302 GVGRGRFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWEALAHGAEVVSYFRWRQAPFAQEQ 361
           G+ +  FWVMEQQPGPVNWA  NP+P PGMVRLW+WEA AHGA  VSYFRWRQAPFAQEQ
Sbjct: 303 GMSKLPFWVMEQQPGPVNWAQWNPAPLPGMVRLWSWEAFAHGAGCVSYFRWRQAPFAQEQ 362

Query: 362 MHAGLHRPDSAPDQGFFEAKRVAEE----LAALALPPVA-QAPVALVFDYEAAWIYEVQP 416
           MHAGL+ PD+  D G  EA +VA E    LAA A    A ++ VALV+DYEA W++E+ P
Sbjct: 363 MHAGLNTPDNRLDVGGSEAAQVASEIRTVLAANAHADAAVRSKVALVYDYEAKWLFEIHP 422

Query: 417 QGAEWSYLGLVYLFYSALRRLGLDVDVVPPGASLRGYAFAVVPSLPIVREEALEAFREAE 476
           QGA++ Y    + +YSALR LGLDVDVVP  ASL GY+  VVP LP+V  +       + 
Sbjct: 423 QGADFHYPRFAFEYYSALRALGLDVDVVPVDASLDGYSLIVVPPLPVVPADLAARLASSG 482

Query: 477 GPVLFGPRSGSKTETFQIPKELPPGPLQALLPLKVVRVESLPPGLLEV----------AE 526
             V+ GPR+GSKT+  QIP  LPPG L  +LPL+V RVES+ P + E            E
Sbjct: 483 AQVVLGPRTGSKTQDLQIPANLPPGALADVLPLRVWRVESMRPNVTEAVRLAGTQDASVE 542

Query: 527 GALGRFPLGLWREWVEA----PLKPLLTFQDGKGALYREGRYLYLAAWPSPELAGRLLSA 582
             + R     WR+++E+        L  F DG+ A  R G + YLA+     L  RL   
Sbjct: 543 DGVARH----WRDFIESKDTNSFDVLARFADGQPAYVRSGAFHYLASLFDDALTTRLFEQ 598

Query: 583 LAAEAGLKVLSLPEGLRLRRRGTWVFAFNYGPEAVEAPASEGARFLLGSRRVGPYDLAVW 642
           +A  AG++ + L E +R+ R G   + FNYG  A     +    F++GS  V P  +AV+
Sbjct: 599 IAQRAGVETVRLGESVRISRCGALTYVFNYGDNAHTITGAADNAFVIGSSTVEPQGVAVY 658


Lambda     K      H
   0.322    0.139    0.454 

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: 1440
Number of extensions: 81
Number of successful extensions: 3
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: 645
Length of database: 661
Length adjustment: 38
Effective length of query: 607
Effective length of database: 623
Effective search space:   378161
Effective search space used:   378161
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.

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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