GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Marivita geojedonensis DPG-138

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_085637757.1 MGEO_RS11955 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q00752
         (377 letters)



>NCBI__GCF_002115805.1:WP_085637757.1
          Length = 365

 Score =  296 bits (759), Expect = 5e-85
 Identities = 167/375 (44%), Positives = 233/375 (62%), Gaps = 25/375 (6%)

Query: 4   LNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELK 63
           L++ ++YK Y  +    ++D ++ I+  +F+V VGPSGCGKST L  +AGLE IT G + 
Sbjct: 5   LDIKNLYKSYGTTE--ILKDINVSIEPGDFLVLVGPSGCGKSTLLNCIAGLEPITGGSIN 62

Query: 64  IDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQIL 123
           I G+ +   +PKDRDIAMVFQ+YALYP M+V  N+ FG+K+R   +   D+++ + AQ L
Sbjct: 63  IGGKDMTHVSPKDRDIAMVFQSYALYPTMTVAKNITFGMKVRGVDQATQDRKLAQVAQQL 122

Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHR 183
            +   L R+P  LSGGQRQRVAMGRA+VRD K+FL DEPLSNLDAKLRV MR EI  +H 
Sbjct: 123 QIEPLLNRRPGQLSGGQRQRVAMGRALVRDPKLFLFDEPLSNLDAKLRVEMRTEIKSLHH 182

Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVA 243
            +GA+ +YVTHDQ EAMTLA +IV+M            G ++Q+G+P E+YNRPAN FVA
Sbjct: 183 NLGASMVYVTHDQIEAMTLATKIVVMKG----------GVIQQIGSPAEIYNRPANLFVA 232

Query: 244 GFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLESKGFKNKNL----IFGIRPED 299
            F+GSPAMN            + +G  I +T    + +     KN++L    I G+RPED
Sbjct: 233 DFMGSPAMNLIPAKAHR----ADEGTRIEITRKSGEPIVLTDTKNRDLPEDVILGVRPED 288

Query: 300 ISSSLLVQETYPDATVDAEVVVS--ELLGSETMLYLKLGQTEFAARVDARDFHEPGEKVS 357
           I+   L      +A   AE ++   E  G++T   ++LG     AR+ A    +PG+   
Sbjct: 289 IADPDL---RGAEAAQAAECLIDMVEPAGADTFAVMQLGGKHVTARLHAETTAKPGQPKR 345

Query: 358 LTFNVAKGHFFDAET 372
           L+F++ K  +F  ET
Sbjct: 346 LSFDLGKVSYFAPET 360


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: 360
Number of extensions: 14
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: 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 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