GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Marinobacter adhaerens HP15

Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate GFF3193 HP15_3135 iron-containing alcohol dehydrogenase

Query= metacyc::STM4044-MONOMER
         (382 letters)



>FitnessBrowser__Marino:GFF3193
          Length = 387

 Score =  265 bits (677), Expect = 2e-75
 Identities = 149/369 (40%), Positives = 218/369 (59%)

Query: 14  GAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNPTE 73
           GAG+   + N  +N       +V+D  +   G +D + + L +  +   ++  V PNP  
Sbjct: 19  GAGSRKSVANFASNFGARHVFLVSDPGVAAAGWVDEIVTLLTDAGIRSTVYTGVSPNPKV 78

Query: 74  ELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVKNAGVPLV 133
           + V  G   Y+S ECD I+A GGGSP+D AK + I+  +      + GV  + N   PL+
Sbjct: 79  DEVMTGAELYKSNECDVIVAIGGGSPMDCAKGIGIVATHGRSILEFEGVDTITNPSPPLI 138

Query: 134 AINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATGMD 193
            I TTAGT+A+++  A+I D  R+ K  II   ++PD+++ D  V   + A +TA TG+D
Sbjct: 139 LIPTTAGTSADVSQFAIISDPNRRFKFSIISKAVVPDVSLIDPEVTETMDAYLTACTGVD 198

Query: 194 ALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGMAF 253
           AL HA+EAYVS G+ PLTD +ALEAIRLIN  L   VD+  +   REQ+      AG+AF
Sbjct: 199 ALVHAIEAYVSTGSGPLTDTHALEAIRLINRNLEPLVDNTADPYLREQIMLASMQAGLAF 258

Query: 254 NSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQAMGVETRGM 313
           ++A LG VHA++H  G   +LPHG+CNA+LL  V  +N  +A  RF R+A+AM ++TRGM
Sbjct: 259 SNAILGAVHAMSHSLGGFLDLPHGLCNALLLEHVVAYNFQSAEDRFRRVAEAMDIDTRGM 318

Query: 314 SDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCNPRTASRDE 373
           +     +  +N I  L +RVG+    ++LGV+  DI      AL DPC   NPR +S  +
Sbjct: 319 AKPEIKKRLMNRIVELKRRVGLEARLAQLGVSVSDIPHLSGFALQDPCILTNPRKSSLRD 378

Query: 374 VRGLYLEAL 382
           V+ +Y EAL
Sbjct: 379 VQVVYEEAL 387


Lambda     K      H
   0.317    0.133    0.384 

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: 438
Number of extensions: 16
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: 382
Length of database: 387
Length adjustment: 30
Effective length of query: 352
Effective length of database: 357
Effective search space:   125664
Effective search space used:   125664
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 (21.7 bits)
S2: 50 (23.9 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