GapMind for catabolism of small carbon sources

 

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

Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate H281DRAFT_04480 H281DRAFT_04480 FAD/FMN-containing dehydrogenase

Query= reanno::Smeli:SMc00832
         (479 letters)



>FitnessBrowser__Burk376:H281DRAFT_04480
          Length = 474

 Score =  177 bits (449), Expect = 7e-49
 Identities = 142/467 (30%), Positives = 215/467 (46%), Gaps = 31/467 (6%)

Query: 27  DLLPEGGLISDERGLKPFETDAFIAYRRMPLAVVLPETTEHVAAVLKYCSRYGIPIVPRG 86
           D +    +++D     P+ TD    Y     AV+ P T + VAA++K    +GI +VP+G
Sbjct: 12  DAIGAAHVLTDAHDTAPYLTDWRRRYTGAACAVLCPATPDEVAALVKLAVEHGIAVVPQG 71

Query: 87  AGTSLSGGAIPQEDAI--VVGLSKMSRTLDIDLFNRTATVQAGVTNLNISDAVSADGFFY 144
             T L+GGA P       VV L +++R  DID  N T TV+AGV    +       G  +
Sbjct: 72  GNTGLAGGATPDSSGAQAVVSLRRLNRVRDIDPHNNTITVEAGVILAEVQKRAEEAGRLF 131

Query: 145 APDPSSQLACTIGGNIGMNSGGAHCLKYGVTTNNLLGVKMVLFDGTVIE-LGGKALDAPG 203
               +++ +CTIGGN+  N+GG   L+YG T    LG+++V   G + + L G   D  G
Sbjct: 132 PLSLAAEGSCTIGGNLATNAGGTGVLRYGNTRELCLGLEVVTPQGELWDGLRGLRKDNTG 191

Query: 204 YDLLGLVCGSEGQLGIVTEATVRLIAKPEGARPVLFGFASSESAGSCVADIIG-----SG 258
           YDL  L  G+EG LGI+T A ++L  +P      L   AS  +A     D +      +G
Sbjct: 192 YDLRDLFIGAEGTLGIITAAVLKLHPQPAARVTALAALASPHAA----LDFLSLTQSVAG 247

Query: 259 IIPVAIEFMDRPAIEIC-EAFAQAGYPLDVEALLIVEVEGSEAEMD----ATLAGIIEIA 313
            +    E M    + +    F Q  YP       IV +E S++E +    A    ++E A
Sbjct: 248 PLLTGFELMSDFCLRLVGRHFEQMRYPFAEPHAQIVLLELSDSESEEHARALFERLMEQA 307

Query: 314 RRHG-VMTIRESQSALEAALIWKGRKSAFGATGRIADYICMDGTVPLSQLSHVLRRTGEI 372
              G V     ++S  ++   W  R+    A       I  D  VP+S++ H +  T   
Sbjct: 308 LEDGMVQDAVVAESLAQSRAFWNLREHIPLAQAEEGLNIKHDIAVPISRIGHFIEETDAA 367

Query: 373 V--AGYGLRVANVFHAGDGNMHPLILYNINDPE---EAARAEAAGNDILKLCVEA----G 423
           +  A  G R+    H GDGN+H    YN+  PE     A  E   + I ++  ++     
Sbjct: 368 IEQAAPGARMVTFGHLGDGNLH----YNVQAPEGVDAKAFLEQYQSPINRVVYDSVHRHR 423

Query: 424 GCLTGEHGVGIEKRDLMLHQYSRADLGQQMAARAAFDPQWLMNPSKV 470
           G ++ EHG+G  K D  +H     ++    A + A DP  LMNP KV
Sbjct: 424 GSISAEHGLGQLKIDEAMHYKPDVEVQLMQAVKRALDPLNLMNPGKV 470


Lambda     K      H
   0.320    0.138    0.404 

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: 567
Number of extensions: 29
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: 479
Length of database: 474
Length adjustment: 33
Effective length of query: 446
Effective length of database: 441
Effective search space:   196686
Effective search space used:   196686
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 (21.8 bits)
S2: 51 (24.3 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