GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Desulfacinum infernum DSM 9756

Align Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein

Query= SwissProt::P19566
         (369 letters)



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  254 bits (649), Expect = 3e-72
 Identities = 148/350 (42%), Positives = 213/350 (60%), Gaps = 15/350 (4%)

Query: 4   VQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFIG 63
           +++R+V K +G V   + ++  + +G+ +V +GPSGCGK+TLLR+IAGLE +TSG + I 
Sbjct: 3   IEIRDVRKDYGRVQAVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIA 62

Query: 64  ETRMNDIPPAERGVGMVFQSYALYPHLSVAENMSFGLKLAGAKKEVMNQRVNQVAEVLQL 123
            T +  +PP +R + MVFQSYAL+PHL+V EN+ FGLK+     + + +R+ +V ++L L
Sbjct: 63  GTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLGL 122

Query: 124 AHLLERKPKALSGGQRQRVAIGRTLVAEPRVFLLDEPLSNLDAALRVQMRIEISRLHKRL 183
           +  L+ KP  LSGG +QRVA+GR ++AE  V L+DEPLSNLDA LR  MR EI  L +RL
Sbjct: 123 SGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRRL 182

Query: 184 GRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMNFLP 243
           G TMIYVTHDQVEAMT+AD+IV++  G++ Q   P   Y  PA+ FVA FIG+P MN +P
Sbjct: 183 GITMIYVTHDQVEAMTMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIVP 242

Query: 244 VKVTATAIEQVQVELPNRQQIWLPVESRGVQVGANMSLGIRPEHLLPSDIADVTLEGEVQ 303
           +  T     Q    L    ++  P    G+     +  GIRPE+L    +A+      V 
Sbjct: 243 LCPT-----QGGAALEPGGRLLFP----GMDPDRYL-FGIRPENL---RLAESGQPAMVT 289

Query: 304 VVEQLGHETQIHIQIPAIRQNLVYRQNDVVLVEEGATFAIGLPPERCHLF 353
             E LG +T +  +I    Q ++ R      + EG    +   P   +LF
Sbjct: 290 GREYLGSDTFVSCEIHG--QEVIVRTRGRRNIREGTVVHLTWDPGDVNLF 337


Lambda     K      H
   0.321    0.138    0.396 

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: 352
Number of extensions: 12
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: 369
Length of database: 365
Length adjustment: 30
Effective length of query: 339
Effective length of database: 335
Effective search space:   113565
Effective search space used:   113565
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: 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