GapMind for catabolism of small carbon sources

 

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

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_002115805.1:WP_085638943.1
          Length = 350

 Score =  310 bits (793), Expect = 5e-89
 Identities = 181/378 (47%), Positives = 239/378 (63%), Gaps = 31/378 (8%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M+ + L+++ KRY   +   +   +LD+ D EF VFVGPSGCGKST LRM+AGLE+ TEG
Sbjct: 1   MSGVTLESVIKRYGQTQ--VIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEG 58

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
            + I  + +    P DR ++MVFQ YALYPHM+V ENM FGLK+  +   DI ++V EA+
Sbjct: 59  TIRIGGRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEAS 118

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
            IL L ++L+RKP  LSGGQRQRVA+GRAIVR  +VFL DEPLSNLDA+LRV MR EIA+
Sbjct: 119 RILKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIAR 178

Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240
           +H+ IGAT IYVTHDQ EAMTLAD+IV++ A          GRIEQ+G P ELY +P N+
Sbjct: 179 LHKEIGATMIYVTHDQVEAMTLADKIVVLRA----------GRIEQVGAPMELYRDPDNR 228

Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDI 300
           FVAGFIGSP+MNF    V+   +V+ DGL  ++ +            G++V +G+RPE +
Sbjct: 229 FVAGFIGSPSMNFIRGRVQGGEVVS-DGLVHSVSK------TASAQEGQEVLIGLRPEHL 281

Query: 301 SSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSH--SPGEKVQL 358
                  E  P +S   D+  +E LG  S  ++  G       V  R  H  S G+ V L
Sbjct: 282 -------ELRPGSSHRVDL--TESLGGVSYAHL-IGPDGEKIIVEERGDHRSSDGDMVDL 331

Query: 359 TFNIAKGHFFDLETEKRI 376
             +      FD +TE R+
Sbjct: 332 VVDPDHMFLFDAKTEARL 349


Lambda     K      H
   0.318    0.135    0.379 

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: 334
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: 350
Length adjustment: 29
Effective length of query: 348
Effective length of database: 321
Effective search space:   111708
Effective search space used:   111708
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