GapMind for catabolism of small carbon sources

 

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

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= BRENDA::Q8NMV1
         (376 letters)



>NCBI__GCF_002115805.1:WP_085638943.1
          Length = 350

 Score =  305 bits (782), Expect = 1e-87
 Identities = 174/375 (46%), Positives = 229/375 (61%), Gaps = 26/375 (6%)

Query: 1   MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60
           M+ VT +     Y   +   +   +L++ DGEF V VGPSGCGKST LRM+AGLE  T+G
Sbjct: 1   MSGVTLESVIKRY--GQTQVIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEG 58

Query: 61  AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120
            I IG +DVT + P DR ++MVFQ YALYPHMTV ENMGF LK+ G +  +I ++V EA+
Sbjct: 59  TIRIGGRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEAS 118

Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180
             L L ++L+RKPKALSGGQRQRVA+GRAIVR P+VFL DEPLSNLDA+LRV+ R +IA 
Sbjct: 119 RILKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIAR 178

Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240
           L +++G T +YVTHDQ EA+T+ D+I VL+ G ++QVGAP ELY  P N FVAGFIGSP+
Sbjct: 179 LHKEIGATMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPS 238

Query: 241 MNLGTFSVKDGDATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSI 300
           MN     V+ G+  S      +S    A    ++   + IG RPE LE+ P         
Sbjct: 239 MNFIRGRVQGGEVVSDGLVHSVSKTASA----QEGQEVLIGLRPEHLELRPGSSH----- 289

Query: 301 PIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGSVFHARIV 360
             ++D  E LG  S  Y  L+G           P+  +I+V    +   + G +    + 
Sbjct: 290 --RVDLTESLGGVS--YAHLIG-----------PDGEKIIVEERGDHRSSDGDMVDLVVD 334

Query: 361 EGGQHNFSASTGKRL 375
                 F A T  RL
Sbjct: 335 PDHMFLFDAKTEARL 349


Lambda     K      H
   0.316    0.135    0.380 

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: 366
Number of extensions: 11
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: 376
Length of database: 350
Length adjustment: 29
Effective length of query: 347
Effective length of database: 321
Effective search space:   111387
Effective search space used:   111387
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 (21.6 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