GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Desulfacinum infernum DSM 9756

Align MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized)
to candidate WP_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein

Query= TCDB::Q00752
         (377 letters)



>NCBI__GCF_900129305.1:WP_073037934.1
          Length = 365

 Score =  259 bits (661), Expect = 1e-73
 Identities = 152/375 (40%), Positives = 214/375 (57%), Gaps = 30/375 (8%)

Query: 2   VELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGE 61
           +++ +  + K Y      +V      ++  + +V +GPSGCGK+T LR++AGLE +T G 
Sbjct: 1   MQIEIRDVRKDYGRVQ--AVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGT 58

Query: 62  LKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQ 121
           + I G  V    P  R+I+MVFQ+YAL+PH++V +N+ FGLK+R    + I++R+K    
Sbjct: 59  IHIAGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVD 118

Query: 122 ILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKI 181
           +LGL+  L+ KP +LSGG +QRVA+GRAI+ +  V LMDEPLSNLDAKLR SMR EI  +
Sbjct: 119 LLGLSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSL 178

Query: 182 HRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKF 241
            RR+G T IYVTHDQ EAMT+ADRIV+M            G++ Q  +P+  Y RPAN F
Sbjct: 179 QRRLGITMIYVTHDQVEAMTMADRIVLMRD----------GQIVQDDSPENFYERPANTF 228

Query: 242 VAGFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLESKGFKNKNLIFGIRPEDIS 301
           VA FIG+P MN   +    G    + G       G+L      G      +FGIRPE++ 
Sbjct: 229 VARFIGTPPMNIVPLCPTQGGAALEPG-------GRLLF---PGMDPDRYLFGIRPENLR 278

Query: 302 SSLLVQETYPDATVDAEVVVSELLGSETMLYLKLGQTEFAARVDARDFHEPGEKVSLTFN 361
              L +   P     A V   E LGS+T +  ++   E   R   R     G  V LT++
Sbjct: 279 ---LAESGQP-----AMVTGREYLGSDTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWD 330

Query: 362 VAKGHFFDAETEAAI 376
               + FDA T+  +
Sbjct: 331 PGDVNLFDARTQERV 345


Lambda     K      H
   0.318    0.135    0.375 

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: 340
Number of extensions: 15
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: 377
Length of database: 365
Length adjustment: 30
Effective length of query: 347
Effective length of database: 335
Effective search space:   116245
Effective search space used:   116245
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