GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Marinobacter adhaerens HP15

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF2762 HP15_2706 inner-membrane translocator

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__Marino:GFF2762
          Length = 291

 Score =  152 bits (385), Expect = 7e-42
 Identities = 90/299 (30%), Positives = 166/299 (55%), Gaps = 14/299 (4%)

Query: 4   FVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAG 63
           F+Q L  G+T+G+ Y L+A+G+T++Y    +INFA G+  M+GG A +     LT++  G
Sbjct: 5   FLQYLFTGITIGATYALIALGFTLIYNASHVINFAQGEFLMIGGMATVS----LTAM--G 58

Query: 64  LPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQ 123
           +P    +++ +V+A+++  +    ++R A  P + +  +  +I  IG SI +    QV  
Sbjct: 59  VP----MILAVVLAVILAGILGVALQRFAIAPAKQADVVTLIIITIGASIFIRGIAQVVW 114

Query: 124 GPRNKPIPPMVSS--VYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQ 181
           G     +    +   +  FG + ++ + + ++ I A+L+        +T +G+A  AT  
Sbjct: 115 GKEYHVMQNFSTDQPIEVFGAV-LNSQSLWVLGIGAILVVGLVLFFTKTLIGKAILATSM 173

Query: 182 DRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVLG 241
           +++ A L+G+     + + F++ A L +VAG + +      S++ G   G+K F AA +G
Sbjct: 174 NKEAARLVGIRTQMVLMLAFMVSALLGSVAGIV-VAPITFTSYDIGIILGLKGFVAAAIG 232

Query: 242 GIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVEKV 300
           G+GS  GAV GGL +G++E++ + Y +  YKD   F+++  VL F P G+ G   VE+V
Sbjct: 233 GLGSGVGAVVGGLSLGIVEAMAAGYISSDYKDAVAFSMILLVLFFMPRGLFGAKVVERV 291


Lambda     K      H
   0.329    0.143    0.421 

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: 287
Number of extensions: 20
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: 300
Length of database: 291
Length adjustment: 26
Effective length of query: 274
Effective length of database: 265
Effective search space:    72610
Effective search space used:    72610
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: 48 (23.1 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