GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Paucidesulfovibrio gracilis DSM 16080

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_900167125.1:WP_200806763.1
          Length = 406

 Score =  236 bits (602), Expect = 8e-67
 Identities = 140/342 (40%), Positives = 200/342 (58%), Gaps = 16/342 (4%)

Query: 21  VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80
           V++ +L I+  E    +GPSGCGKTT LRMIAGLE  T+G++YI  RR+ND P   R++ 
Sbjct: 60  VQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIYIKGRRINDTPIHKRNLG 119

Query: 81  MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140
           M+FQNYAL+PH T+++N+AFGLK R V + E+  +V +A +++ +  +  R    LSGGQ
Sbjct: 120 MIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMVRLPGVEKRYASQLSGGQ 179

Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200
           +QR+AL RAIV EP V LMDEPLS LD KLR +MR EI  + Q+L  T ++VTHDQ EA+
Sbjct: 180 QQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQQLNLTTLFVTHDQREAL 239

Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQ--DGDAFYFR 258
           +M ++IVVM+DG  QQ  TP+ VY  P N FVA F+G    NF    +++  D D    R
Sbjct: 240 SMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLGH--ANFFDARVLEVLDNDQVRVR 297

Query: 259 -APSISLRLPE-GRYGVLKASGAIGKPVVLGVRPEDLHDEEVFMTT---YPDSVLQMQVE 313
            A  +       GR+   +    + +   + V   DL DEE+  T    YP  +      
Sbjct: 298 IAEGLEFTADHVGRWRQGQDVHLVMRAQKINVTSPDLADEELESTDLNYYPGKIYDR--- 354

Query: 314 VVEHMGSEV--YLHTSIGPNTIVARVNPRHVYHVGSSVKLAI 353
              +MG E   ++  + G    +  +  R  + +G  V L +
Sbjct: 355 --SYMGGETSYFVELANGVRLHIISMVRRRPHRIGDEVVLHV 394


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: 418
Number of extensions: 18
Number of successful extensions: 1
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: 406
Length adjustment: 31
Effective length of query: 353
Effective length of database: 375
Effective search space:   132375
Effective search space used:   132375
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