GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Magnetospirillum magneticum AMB-1

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_043743902.1 AMB_RS08455 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>NCBI__GCF_000009985.1:WP_043743902.1
          Length = 291

 Score =  166 bits (419), Expect = 8e-46
 Identities = 95/298 (31%), Positives = 156/298 (52%), Gaps = 12/298 (4%)

Query: 4   FVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAG 63
           F+Q L +GLT G+IY L  +G+ ++Y    +INFA G+  M+GG A   +      I+  
Sbjct: 5   FLQYLFSGLTSGAIYALAGLGFAIIYNASHVINFAQGEFIMIGGMATATMVAAGVPIYLA 64

Query: 64  LPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQ 123
           +P+A+   +++ VAM          E+ A  P R +  +  +I  IG SI +    Q+  
Sbjct: 65  IPLAMAASMLVGVAM----------EKFAIEPARNADVVTIIIITIGASIFMRGAAQLIW 114

Query: 124 GPRNKPIPPMVSSV-YQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRATEQD 182
                 +P             ++  + + +  I+AV + + WY  NRT  G+A   T  +
Sbjct: 115 DKEFHSLPAFSGETPIAVMGATLMPQSLWVFGISAVAIALLWYFFNRTMFGKAMLGTSHN 174

Query: 183 RKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAVLGG 242
           R  A L+GV V + +  +F + A L AV G + +      ++  G   G+K F+AAVLGG
Sbjct: 175 RLAAQLVGVAVKRVLLASFALSALLGAVGGIV-VTPITFTNYEAGIMLGLKGFSAAVLGG 233

Query: 243 IGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVEKV 300
           +G+  GA+ GGL++G+ E++ S Y + AYKD   F I+ FVL F P+G+ G+   ++V
Sbjct: 234 LGNGTGAIIGGLIVGIAEAMASGYLSSAYKDAIAFIIILFVLFFMPSGLFGKRGTDRV 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: 267
Number of extensions: 15
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.

Links

Downloads

Related tools

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