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_092482139.1 BM299_RS03860 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_900115975.1:WP_092482139.1
          Length = 390

 Score =  159 bits (401), Expect = 2e-43
 Identities = 84/255 (32%), Positives = 146/255 (57%), Gaps = 12/255 (4%)

Query: 21  VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKD---- 76
           +++ +  +++ E  V +G SG GK+T +R +  L   T G +Y+    + +   K     
Sbjct: 44  IRNASFQVEEGEVFVIMGLSGSGKSTLIRCLNLLNKPTAGEIYVDGDNILEYDKKQLKKF 103

Query: 77  --RDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPK 134
               +AMVFQ++ L  H TV  N+ +GL+++K+PK E     ++A     +A   ++ P 
Sbjct: 104 RQEKVAMVFQHFGLLSHRTVIGNVEYGLEVKKIPKNERCEIAKKAIANAGLAGWENKMPN 163

Query: 135 ALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTH 194
            LSGG +QRV L RA+  +P + LMDEP S LD  +R  M+ E+ +L  RL+ T+I++TH
Sbjct: 164 ELSGGMQQRVGLARALANDPDILLMDEPFSALDPLIRRDMQYELMELQSRLKKTIIFITH 223

Query: 195 DQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQDGDA 254
           D  EA  +GDR+ VM+DGVI+Q  TP+ + + P++ ++  F+     +  R +++Q    
Sbjct: 224 DINEAFKIGDRVAVMKDGVIEQIGTPEELLASPESEYIENFV----KDIDRSKVLQAKHV 279

Query: 255 FYFRAPSISLRLPEG 269
            +   P++ + + EG
Sbjct: 280 MF--KPTVLVSIKEG 292


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: 295
Number of extensions: 10
Number of successful extensions: 2
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: 384
Length of database: 390
Length adjustment: 30
Effective length of query: 354
Effective length of database: 360
Effective search space:   127440
Effective search space used:   127440
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: 50 (23.9 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