GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Herbaspirillum seropedicae SmR1

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate HSERO_RS22475 HSERO_RS22475 3-oxoacyl-ACP reductase

Query= reanno::acidovorax_3H11:Ac3H11_614
         (280 letters)



>FitnessBrowser__HerbieS:HSERO_RS22475
          Length = 263

 Score =  224 bits (570), Expect = 2e-63
 Identities = 111/252 (44%), Positives = 159/252 (63%), Gaps = 2/252 (0%)

Query: 29  AKFPSLQGRAVFVTGGGSGIGAAIVAAFAEQGARVAFVDVAREASEALAQHIADAGLPRP 88
           A + SL G+ V +TGGGSGIGAA+V AF  QGA+V F+D+A E S+AL   + DA +  P
Sbjct: 12  ALYRSLAGKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIAAEPSQALVASLKDAPIA-P 70

Query: 89  WWRVCDVRDVQALQACMADAAAELGSDFAVLVNNVASDDRHTLESVTPEYYDERMAINER 148
            +  C++ +++AL+A   +    +G    +L+NN A+DDRH    VTP Y+DER+A+N R
Sbjct: 71  RFFPCNLMNLEALRATFTEIETVMGG-VDILINNAANDDRHKTADVTPAYWDERLAVNLR 129

Query: 149 PAFFAIQAVVPGMRRLGAGSVINLGSTGWQGKGTGYPCYAIAKSSVNGLTRGLAKTLGQD 208
             FF  QAV+PGMR    G ++N GS  W         Y  AK+ + G+T G+A+  G+D
Sbjct: 130 HQFFCAQAVLPGMRERKQGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRD 189

Query: 209 RIRINTVSPGWVMTERQIKLWLDAEGEKELARNQCLPDKLRPHDIARMVLFLASDDAAMC 268
            +R+N + PG + T RQ  LW   E E ++   QCLP ++ PHD+A + LFL+SD  A C
Sbjct: 190 GVRVNAIIPGAIRTPRQTLLWHTPEEEAKILAAQCLPTRVDPHDVAALALFLSSDSGAKC 249

Query: 269 TAQEFKVDAGWV 280
           T +E+ VDAGW+
Sbjct: 250 TGREYYVDAGWL 261


Lambda     K      H
   0.320    0.133    0.405 

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: 180
Number of extensions: 7
Number of successful extensions: 1
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: 280
Length of database: 263
Length adjustment: 25
Effective length of query: 255
Effective length of database: 238
Effective search space:    60690
Effective search space used:    60690
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: 47 (22.7 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