GapMind for catabolism of small carbon sources

 

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

Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate H281DRAFT_02777 H281DRAFT_02777 alpha-glucosidase

Query= uniprot:A8LLL3
         (552 letters)



>FitnessBrowser__Burk376:H281DRAFT_02777
          Length = 524

 Score =  435 bits (1118), Expect = e-126
 Identities = 223/492 (45%), Positives = 300/492 (60%), Gaps = 15/492 (3%)

Query: 19  WWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKDFGYD 78
           WW+  VIYQ+YPRSFQDSNGDGIGDL GI  R+PY+A LG+DA+W+SP + SPM DFGYD
Sbjct: 6   WWQRGVIYQVYPRSFQDSNGDGIGDLAGITSRLPYLAGLGIDAVWLSPIYPSPMADFGYD 65

Query: 79  ISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDNPKAD 138
           ++DY D+DPMFG+L DF    + AH  GL+V++D V +H+SD+HPWFEESRSSR+NPK D
Sbjct: 66  VADYCDIDPMFGTLGDFKQFADRAHELGLKVLLDFVPNHSSDRHPWFEESRSSRENPKRD 125

Query: 139 WYVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLTSQPDLNFHCADVQDALLG 198
           WY+W D  PDG PPNNWLS  GGS W WD R  QYY H FL  QPDLN+    V+ A+  
Sbjct: 126 WYLWRDPAPDGGPPNNWLSRMGGSAWEWDERTGQYYYHAFLREQPDLNWRNPQVRRAMDD 185

Query: 199 VGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPEERNSNIAPEVNPYNHQRHLYSKNQ 258
           V RFWLDRGVDGFR+D +   + D++ RDNPP P  E      P    ++ Q   Y+++Q
Sbjct: 186 VLRFWLDRGVDGFRVDVLWLLIKDSQFRDNPPNPAYE------PGQPEHHRQLQTYTEDQ 239

Query: 259 PENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILGQYTRGETGVHMCYAFEFLAQEKL 318
           PE  E +   RA ++EY     +GE+       +++  Y     G  M + F+ L     
Sbjct: 240 PEVHEIVRSMRATLDEYGERVLIGEI--YLPVPQLVRYYGANGDGADMPFNFQLL-NAAW 296

Query: 319 TAKRVAEVLNKVDE-VASDGWACWAFSNHDVMRHVSRWDLTPGAQRGMLTLLMCLRGSVC 377
            A  +A ++   D  +    W  W   NHD  R  SR  +     R    LL+ LRG+  
Sbjct: 297 NAGEIARMIRDYDSALPVHAWPNWVLGNHDNPRVASR--VGAAQARVAAVLLLTLRGTPT 354

Query: 378 LYQGEELGLPEAEVAFDDLQDPYGIEFWPEYKGRDGCRTPMVWQSDNMSGGFSIHRPWLP 437
           LY G+E+G+ + E++ D +QDP  I      +GRD  RTPM W +     GF+  R WLP
Sbjct: 355 LYYGDEIGMTDGEISPDRVQDPAEIRQPDIGQGRDPERTPMQWDAALPGAGFTNGRSWLP 414

Query: 438 VSTEHLGLAVAVQEEAPDALLHHYRRALAFRRAHPALVKGDISDVTVVGDVISFLRKDPE 497
           +ST+    +V  Q+  P ++L  YRR L  RR++ ALV+G I +V   GDV++F R    
Sbjct: 415 ISTD---TSVRAQDGDPSSMLSLYRRLLELRRSNAALVQGAIENVAASGDVLTFERHYRG 471

Query: 498 ETVFVAINMSDA 509
           + +F+A+NM  A
Sbjct: 472 QRLFIALNMGAA 483


Lambda     K      H
   0.321    0.138    0.451 

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: 1015
Number of extensions: 58
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: 552
Length of database: 524
Length adjustment: 35
Effective length of query: 517
Effective length of database: 489
Effective search space:   252813
Effective search space used:   252813
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: 52 (24.6 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