GapMind for catabolism of small carbon sources

 

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

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate H281DRAFT_02299 H281DRAFT_02299 aldehyde dehydrogenase

Query= metacyc::MONOMER-16244
         (495 letters)



>FitnessBrowser__Burk376:H281DRAFT_02299
          Length = 506

 Score =  352 bits (904), Expect = e-101
 Identities = 205/484 (42%), Positives = 281/484 (58%), Gaps = 17/484 (3%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83
           FI  E+V+    + F  VSP T E  T +  +   D++ A++AA  A  ++W  +    R
Sbjct: 22  FIGGEWVKPAGGEYFDNVSPITGEPFTSIPRSREADVELALDAAHRA-KAAWGKTSTTDR 80

Query: 84  MKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKGDVALTAAYFRSCAGWTDKIKGSVI 142
             +L ++AD ++ +   LA  E +DNGK L      D+ L   +FR  AG     +GS+ 
Sbjct: 81  ANILNRIADRMEANLQRLAVAETIDNGKPLRETMAADIPLAIDHFRYFAGAVRAQEGSIS 140

Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202
           E  D    Y   EP+GV GQIIPWNFP+LMA WKL P L  G   VLK AE TP S L L
Sbjct: 141 EIDDDTVAYHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQTPASILVL 200

Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262
             LI++   P GV+NVV+GFG  AG P++S  +I K+AFTG T TGR IM+ A++ N+  
Sbjct: 201 VELIQDL-LPAGVLNVVNGFGLEAGKPLASSKRIAKIAFTGETTTGRLIMQYASQ-NIIP 258

Query: 263 VTLELGGKSPNIVF------DDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKI 316
           VTLELGGKSPNI F      DD+     ++        N GEVC   SR+ + E IYD  
Sbjct: 259 VTLELGGKSPNIFFADVMNQDDSYFDKALEGFAM-FALNQGEVCTCPSRVLIDEKIYDSF 317

Query: 317 VSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFG--- 373
           +        ++  G P    T +GAQ SQ QL+KIL Y+D+GK+EGA  + GGER     
Sbjct: 318 MERALKRVAAITQGHPLDTRTMIGAQASQEQLEKILSYVDLGKQEGAECLIGGERNTLSG 377

Query: 374 --NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHT 431
             +KGY++KPT+F    +  +I ++EIFGPVV++T FKT EE + +AND+ YGL AGV T
Sbjct: 378 ELSKGYYVKPTVFRGHNK-MRIFQEEIFGPVVSVTTFKTEEEALEIANDTLYGLGAGVWT 436

Query: 432 TNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRI 491
            + + A     +I +G +W N Y+ +     FGGY QSGIGRE  +  LD+Y Q K + +
Sbjct: 437 RDGTRAYRFGRQIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKNLLV 496

Query: 492 GLSQ 495
             S+
Sbjct: 497 SYSE 500


Lambda     K      H
   0.316    0.133    0.389 

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: 587
Number of extensions: 24
Number of successful extensions: 8
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: 495
Length of database: 506
Length adjustment: 34
Effective length of query: 461
Effective length of database: 472
Effective search space:   217592
Effective search space used:   217592
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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