GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Sphingomonas koreensis DSMZ 15582

Align Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized)
to candidate Ga0059261_3648 Ga0059261_3648 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= SwissProt::Q9NKW1
         (441 letters)



>FitnessBrowser__Korea:Ga0059261_3648
          Length = 298

 Score =  254 bits (649), Expect = 3e-72
 Identities = 141/296 (47%), Positives = 184/296 (62%), Gaps = 7/296 (2%)

Query: 1   MALNFKDKVVIVTGAGGGIGKVYALEFAKRGAKVVVNDLGGSHTGQGSSSKAADKVVEEI 60
           MA+ F  +V IVTGAGGG+G+ YALE A+RGA+VVVNDLGGS  G G S  AA KVVEEI
Sbjct: 1   MAIRFDGRVAIVTGAGGGLGRAYALELARRGARVVVNDLGGSRDGTGHSDAAA-KVVEEI 59

Query: 61  KAAGGTAVANYDSVEDG---EKIVQTAMDSFGGVDILINNAGILRDVSFGKMTDGDWDLV 117
           +A GG A+AN  SV D    E +V  A + +GGV ILINNAG+LRD SF  M   D+  V
Sbjct: 60  EALGGEALANGGSVTDYAQMEAMVAAAKEKWGGVHILINNAGVLRDKSFANMEPEDFRFV 119

Query: 118 YRVHAKGAYKLSRAAWNHMREKNFGRIIMTSSAAGLYGNFGQANYGSMKMALVGLSNTLA 177
             VH  G+  +++A W+ MR++N+GRI+MT+S+ GLYGNFGQANYG+ K+ L GL+ TL 
Sbjct: 120 VDVHLNGSANVTKAVWSTMRDQNYGRILMTASSTGLYGNFGQANYGAAKLGLAGLTKTLY 179

Query: 178 QEGKSKNIHCNTIAPIAASRLTESVMPPEILEQMKPDYIVPLVLYLCHQDTTETGGVFEV 237
            EG   +I  NTIAP A +R+TE + P    +   P+ + P  L+L  +D   T  +   
Sbjct: 180 LEGAKYDIRVNTIAPTAGTRMTEDIFPEAAFQAFTPESVAPAALFLVSED-APTNMIVGA 238

Query: 238 GAGWVSKVRLQRSAGVYM--KDLTPEKIKDNWAQIESFDNPSYPTSASESVSGILA 291
           GAG      +  + GV +  +DLTPE I  NW+ I        P S  E    I+A
Sbjct: 239 GAGVFQAAYITLTPGVRLEGEDLTPEGIAANWSAITDRMGEIVPKSGGEQAMTIMA 294


Lambda     K      H
   0.313    0.131    0.371 

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: 356
Number of extensions: 22
Number of successful extensions: 4
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: 441
Length of database: 298
Length adjustment: 29
Effective length of query: 412
Effective length of database: 269
Effective search space:   110828
Effective search space used:   110828
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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