GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Pseudomonas fluorescens FW300-N2C3

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate AO356_08345 AO356_08345 urea ABC transporter permease

Query= TCDB::P74318
         (286 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_08345
          Length = 500

 Score =  121 bits (304), Expect = 3e-32
 Identities = 86/287 (29%), Positives = 147/287 (51%), Gaps = 15/287 (5%)

Query: 8   FNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANT-------SGINLW 60
           F+G+++GSI+ L A+GL +T+G+L + N AHG+ + L AY T+           + I  +
Sbjct: 209 FSGMSLGSILLLAALGLAITFGLLGVINMAHGEMLMLGAYSTYVVQLLFQRFAPNAIEFY 268

Query: 61  LSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIWGGNNQN 120
             +AL  V   I   IG  L    +R         ++ + G++L L   + L++G  N  
Sbjct: 269 PLIALP-VAFFITAAIGMALERTVIRHLYGRPLETLLATWGISLMLIQLVRLVFGAQNVE 327

Query: 121 YRVPIVPA---QDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADNVDLA 177
              P   +   Q    +   Y R+++IA A+  +V+  L+L +T++G  +RAV  N ++A
Sbjct: 328 VANPAWLSGGIQVLPNLVLPYNRIVIIAFALFVVVLTWLLLNKTRLGLNVRAVTQNRNMA 387

Query: 178 KVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASVILGGIGNPY 237
              G+    V M  + + + +  LGG     +  + P++G   I+  F  V+LGG+G   
Sbjct: 388 ACCGVPTGRVDMLAFGLGSGIAGLGGVALSQIGNVGPDLGQSYIIDSFLVVVLGGVGQLA 447

Query: 238 GAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFI--RPQGLF 282
           G++     +G+A ++  P  G    +G  L+L +IILFI  RPQGLF
Sbjct: 448 GSVFAAFGLGIANKILEPQIGA--VLGKILILALIILFIQKRPQGLF 492


Lambda     K      H
   0.329    0.143    0.450 

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: 291
Number of extensions: 11
Number of successful extensions: 3
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: 286
Length of database: 500
Length adjustment: 30
Effective length of query: 256
Effective length of database: 470
Effective search space:   120320
Effective search space used:   120320
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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