GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Desulfoscipio geothermicus DSM 3669

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_900115975.1:WP_092484009.1
          Length = 344

 Score =  210 bits (534), Expect = 6e-59
 Identities = 106/271 (39%), Positives = 168/271 (61%), Gaps = 6/271 (2%)

Query: 23  DFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIAMV 82
           D NL++Q+ E+ + +GP+G GKT  L  IAG+    +G +   +R +  + P+ R +  V
Sbjct: 18  DINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFKERNLATLAPEQRKVGFV 77

Query: 83  FQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQRQ 142
           +Q+YAL+PH+TV +N+ FG ++RK+PK  I  ++ E   +L I HLL+R P  LSGG++Q
Sbjct: 78  YQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGIGHLLNRHPSTLSGGEQQ 137

Query: 143 RVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAMTM 202
           R AL RA++  P++ L+DEPLS LD + +   + E++K+HQ L+TT ++VTHD  EAM +
Sbjct: 138 RTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTLKTTTLHVTHDFNEAMYL 197

Query: 203 GDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQDGDAFYFRAPSI 262
            D+I VM  G I Q  TPQ ++ +P+N FVA F+G    N   G++  D  +    AP +
Sbjct: 198 ADKIGVMHQGQIIQVGTPQEIFYKPQNDFVASFVG--IENIFEGQVNDDKVSL---APDV 252

Query: 263 SLRLPEGRYGVLKASGAIGKPVVLGVRPEDL 293
            + +  G+ G +K +    + + L   P DL
Sbjct: 253 DIFVNTGKQGKVKVA-VPPEDIALSKEPFDL 282


Lambda     K      H
   0.321    0.138    0.395 

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: 320
Number of extensions: 17
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 384
Length of database: 344
Length adjustment: 29
Effective length of query: 355
Effective length of database: 315
Effective search space:   111825
Effective search space used:   111825
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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