GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK_Bb in Bacteroides thetaiotaomicron VPI-5482

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate 353166 BT3640 lipoprotein releasing system ATP-binding protein (NCBI ptt file)

Query= uniprot:Q6MNM2
         (347 letters)



>lcl|FitnessBrowser__Btheta:353166 BT3640 lipoprotein releasing
           system ATP-binding protein (NCBI ptt file)
          Length = 218

 Score =  144 bits (363), Expect = 2e-39
 Identities = 83/217 (38%), Positives = 122/217 (56%), Gaps = 7/217 (3%)

Query: 4   IQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISID 63
           I+   I KSFGS  VLKGIDL+I  GE + +VGPSG GK+TLL+ +  L+  D+GT++ID
Sbjct: 2   IKLEGITKSFGSLQVLKGIDLEINKGEIVSIVGPSGAGKTTLLQIMGTLDEPDAGTVAID 61

Query: 64  GKKINDIEPQ------NRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEI 117
           G  ++ ++ +      N++I  VFQ + L P  T  EN+     +  +++ E  +R  EI
Sbjct: 62  GTVVSRMKEKELSAFRNKNIGFVFQFHQLLPEFTALENVMIPAFIAGVSSKEANERAMEI 121

Query: 118 SELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIK 177
              + +      KP ELSGG++QRVA+ RAL     VIL DEP  +LD H +  +     
Sbjct: 122 LAFMGLTDRASHKPNELSGGEKQRVAVARALINHPAVILADEPSGSLDTHNKEDLHQLFF 181

Query: 178 RLHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQ 214
            L      T + VTHD+  A  + DR   + DG I++
Sbjct: 182 DLRDRLGQTFVIVTHDEGLA-KITDRTVHMVDGTIKK 217


Lambda     K      H
   0.318    0.136    0.383 

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: 175
Number of extensions: 8
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: 347
Length of database: 218
Length adjustment: 25
Effective length of query: 322
Effective length of database: 193
Effective search space:    62146
Effective search space used:    62146
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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