GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Pseudovibrio axinellae Ad2

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_068010540.1 PsAD2_RS21550 ABC transporter ATP-binding protein

Query= TCDB::Q00752
         (377 letters)



>NCBI__GCF_001623255.1:WP_068010540.1
          Length = 370

 Score =  312 bits (799), Expect = 1e-89
 Identities = 177/390 (45%), Positives = 243/390 (62%), Gaps = 35/390 (8%)

Query: 1   MVELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKG 60
           M  +++ H  K + ++    ++D  LD+K+ EF+V +G SGCGKST L ++AGLE +  G
Sbjct: 1   MATISIEHASKSFGSTK--VLKDISLDVKDGEFLVLLGASGCGKSTLLNIIAGLEPMADG 58

Query: 61  ELKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAA 120
            +++DGEVVND  PK+RDIAMVFQ+YALYP+M+V  N+AFGL++R  SK      V+E A
Sbjct: 59  TIRLDGEVVNDVHPKNRDIAMVFQSYALYPNMTVERNIAFGLEMRKISKAERKATVREVA 118

Query: 121 QILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 180
             L +   L RKP+ LSGGQRQRVAMGRA+VR  K+FL DEPLSNLDAKLR  MR EI K
Sbjct: 119 STLQIEHLLSRKPSQLSGGQRQRVAMGRALVRRPKIFLFDEPLSNLDAKLRGEMRTEIKK 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANK 240
           +H+ + AT +YVTHDQ EAMTLADRI IM            G ++Q+GTPQE+Y++PAN 
Sbjct: 179 LHQTLKATMVYVTHDQIEAMTLADRIAIMKD----------GEIQQIGTPQEIYSKPANM 228

Query: 241 FVAGFIGSPAMNFFDVTIKDGHLVSKD----GLTIAVTEGQ----------LKMLESKGF 286
           +VAGF+G+P MNF +V      LV ++     +  AV +G+           K LE++  
Sbjct: 229 YVAGFVGAPPMNFVEV-----DLVKREEQLGAILPAVLKGEPVDHFLPLPNSKHLEAR-- 281

Query: 287 KNKNLIFGIRPEDISSSLLVQETYPDATVDAEVVVSELLGSETMLYLKLGQTEFAARVDA 346
           +N  +I G+RPE I+ S     + P+   D E +  E  G++T+  ++L      ARV  
Sbjct: 282 ENTKVILGLRPEIITDSTSTHSSAPEIECDVEFL--EPTGADTLCIIRLNGHPAKARVSP 339

Query: 347 RDFHEPGEKVSLTFNVAKGHFFDAETEAAI 376
                PGE +  T +  +   FD  TE AI
Sbjct: 340 LFACPPGESMRFTLDTHRACLFDPTTEQAI 369


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: 371
Number of extensions: 11
Number of successful extensions: 4
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: 370
Length adjustment: 30
Effective length of query: 347
Effective length of database: 340
Effective search space:   117980
Effective search space used:   117980
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. 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