GapMind for catabolism of small carbon sources

 

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

Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_043743902.1 AMB_RS08455 branched-chain amino acid ABC transporter permease

Query= TCDB::P21627
         (307 letters)



>NCBI__GCF_000009985.1:WP_043743902.1
          Length = 291

 Score =  152 bits (383), Expect = 1e-41
 Identities = 93/303 (30%), Positives = 163/303 (53%), Gaps = 18/303 (5%)

Query: 7   YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66
           +LQ L +GLT G+ YAL  +G+ ++Y    +INFA GE  MIG     +A   +   G+ 
Sbjct: 5   FLQYLFSGLTSGAIYALAGLGFAIIYNASHVINFAQGEFIMIGG----MATATMVAAGVP 60

Query: 67  SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQD 126
            + L +  A AAS++V    G ++E+ A  P R  + +  +I  IG SIF++ A  L  D
Sbjct: 61  -IYLAIPLAMAASMLV----GVAMEKFAIEPARNADVVTIIIITIGASIFMRGAAQLIWD 115

Query: 127 SKEKAIPTLLPGNFVFGES--SMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACR 184
            +  ++P         GE+  ++ G  +    + +F ++ + +  L  F +R+  G+A  
Sbjct: 116 KEFHSLPAFS------GETPIAVMGATLMPQSLWVFGISAVAIALLWYFFNRTMFGKAML 169

Query: 185 ACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTA 244
             + +     L+G+    ++  +F + A L AV  +++       N   G + G+K F+A
Sbjct: 170 GTSHNRLAAQLVGVAVKRVLLASFALSALLGAVGGIVV-TPITFTNYEAGIMLGLKGFSA 228

Query: 245 AVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEV 304
           AVLGG+G+  GA++GGL++G+AEA  +      YKD +AF +++ VL F P+G+ G+   
Sbjct: 229 AVLGGLGNGTGAIIGGLIVGIAEAMASGYLSSAYKDAIAFIIILFVLFFMPSGLFGKRGT 288

Query: 305 EKV 307
           ++V
Sbjct: 289 DRV 291


Lambda     K      H
   0.328    0.145    0.413 

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: 262
Number of extensions: 14
Number of successful extensions: 4
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: 307
Length of database: 291
Length adjustment: 27
Effective length of query: 280
Effective length of database: 264
Effective search space:    73920
Effective search space used:    73920
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 (21.7 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