GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Desulfacinum infernum DSM 9756

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  276 bits (707), Expect = 5e-79
 Identities = 157/349 (44%), Positives = 210/349 (60%), Gaps = 21/349 (6%)

Query: 21  VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIA 80
           V+  +  +++ +  V +GPSGCGKTT LR+IAGLE +T G ++I    V  +PP  R+I+
Sbjct: 18  VRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGTIHIAGTDVTHLPPVKRNIS 77

Query: 81  MVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPKALSGGQ 140
           MVFQ+YAL+PH+ V +N+ FGLK+RKVP  EI+RR++    +L ++  LD KP  LSGG 
Sbjct: 78  MVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVDLLGLSGRLDSKPGELSGGM 137

Query: 141 RQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTEAM 200
           +QRVALGRAI+ E  V LMDEPLSNLDAKLR  MR EI  L +RL  T+IYVTHDQ EAM
Sbjct: 138 QQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSLQRRLGITMIYVTHDQVEAM 197

Query: 201 TMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQDGDAFYFRAP 260
           TM DRIV+MRDG I Q D+P+  Y +P N FVA FIG+P MN +     Q G A      
Sbjct: 198 TMADRIVLMRDGQIVQDDSPENFYERPANTFVARFIGTPPMNIVPLCPTQGGAALE---- 253

Query: 261 SISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFMTTYPDSVLQMQVEVVEHMGS 320
                 P GR   L   G      + G+RPE+L           +S     V   E++GS
Sbjct: 254 ------PGGR---LLFPGMDPDRYLFGIRPENLR--------LAESGQPAMVTGREYLGS 296

Query: 321 EVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNKIHIFDAETEESI 369
           + ++   I    ++ R   R     G+ V L  D   +++FDA T+E +
Sbjct: 297 DTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWDPGDVNLFDARTQERV 345


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: 347
Number of extensions: 14
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: 384
Length of database: 365
Length adjustment: 30
Effective length of query: 354
Effective length of database: 335
Effective search space:   118590
Effective search space used:   118590
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