GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Bb in Geotalea uraniireducens Rf4

Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein

Query= uniprot:Q6MNM2
         (347 letters)



>NCBI__GCF_000016745.1:WP_011938227.1
          Length = 353

 Score =  211 bits (537), Expect = 2e-59
 Identities = 117/257 (45%), Positives = 165/257 (64%), Gaps = 12/257 (4%)

Query: 1   MAKIQFS--NIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSG 58
           M  I+ S  ++  + G   +LKG+ LD+  GE + L+GPSG GK+TLLR++AGLE    G
Sbjct: 1   MTSIELSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHG 60

Query: 59  TISI-------DGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEIT 111
           +I I         KKI ++  + R +  VFQSYAL+PH TV EN+ +GLKL+ +   EI 
Sbjct: 61  SIRIGEQMVFESAKKI-EVSVEKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIR 119

Query: 112 KRVNEISELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQ 171
           +RV E+   L +  L +R P +LSGGQ+QRVAL R+L     VIL DEPLSNLDA LR +
Sbjct: 120 QRVQEVLANLGLGDLSERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREE 179

Query: 172 MRLEIKRLHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIA 231
            R+ +++L  +   + + VTHDQ EA  + D++ +LKDGVIEQ GTP E+Y  PK+ F+A
Sbjct: 180 ARIWLRQLIIDLNLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVA 239

Query: 232 TFIGSPEMNFLEGAVLE 248
            F+G+   N + G V +
Sbjct: 240 EFMGA--NNTISGLVTD 254


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: 298
Number of extensions: 19
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: 353
Length adjustment: 29
Effective length of query: 318
Effective length of database: 324
Effective search space:   103032
Effective search space used:   103032
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: 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