GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Thiothrix lacustris DSM 21227

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  237 bits (605), Expect = 3e-67
 Identities = 133/288 (46%), Positives = 183/288 (63%), Gaps = 8/288 (2%)

Query: 6   LEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIG 65
           L +I K +  Q    + DFNL IQD EF   +GPSGCGKTT LR+IAG E   EG + + 
Sbjct: 9   LSNISKRFASQE--VLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLN 66

Query: 66  DRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDI 125
              +  +P + R    VFQ+YAL+PH+TV+ N+AFGLK+  V   +I  RV +A  I+ +
Sbjct: 67  GDDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRL 126

Query: 126 AHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRL 185
           +    RKP  LSGGQ+QRVA+ RA+V  P++ L+DE LS LD KLR QM+ E+++L ++L
Sbjct: 127 SEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQL 186

Query: 186 QTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIR 245
             T +YVTHDQ EA++M DRI+VM +G  QQ  TP+ +Y  P+N+FVA FIG   +N   
Sbjct: 187 GITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIGE--INVFD 244

Query: 246 GEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDL 293
           GEIVQ    + + A SI+  + E R        A+G  V + +RPEDL
Sbjct: 245 GEIVQALGEYQYEA-SINGVVREIR---CDHRFAVGDKVHVMLRPEDL 288



 Score = 24.3 bits (51), Expect = 0.006
 Identities = 9/32 (28%), Positives = 20/32 (62%)

Query: 339 PRHVYHVGSSVKLAIDLNKIHIFDAETEESIG 370
           PR +Y    ++ +A  + +I++FD E  +++G
Sbjct: 221 PREIYESPRNLFVAQFIGEINVFDGEIVQALG 252


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: 338
Number of extensions: 16
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: 2
Length of query: 384
Length of database: 369
Length adjustment: 30
Effective length of query: 354
Effective length of database: 339
Effective search space:   120006
Effective search space used:   120006
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