GapMind for catabolism of small carbon sources

 

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

Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::O30494
         (367 letters)



>NCBI__GCF_002115805.1:WP_085638943.1
          Length = 350

 Score =  377 bits (969), Expect = e-109
 Identities = 198/353 (56%), Positives = 256/353 (72%), Gaps = 11/353 (3%)

Query: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60
           M+ + ++++ K +    +I G+DL+V D EF VFVGPSGCGKSTLLR++AGLEE +EGTI
Sbjct: 1   MSGVTLESVIKRYGQTQVIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEGTI 60

Query: 61  ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKQLVESKVNEAARI 120
            + GRD+T + P+ R ++MVFQTYALYPHM+V +NM F L + G   + ++ KV EA+RI
Sbjct: 61  RIGGRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEASRI 120

Query: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180
           L+L   L+RKPK LSGGQRQRVAIGRAIVR P++FLFDEPLSNLDA LRV+MR+E+ARLH
Sbjct: 121 LKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARLH 180

Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240
           KE+ ATMIYVTHDQVEAMTLADK+VVL +GRIEQVG+P+ELY  P N FVAGF+G+P M 
Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPSMN 240

Query: 241 FLKGKVTRVDGQGCEVQLDAGTLISLPLSGASLSVGSAVTLGIRPEHLEIASPGQTTLTV 300
           F++G+V     QG EV  D   L+      AS   G  V +G+RPEHLE+  PG +    
Sbjct: 241 FIRGRV-----QGGEVVSDG--LVHSVSKTASAQEGQEVLIGLRPEHLEL-RPGSSH--- 289

Query: 301 TADVGERLGSDTFCHVITSNGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFD 353
             D+ E LG  ++ H+I  +GE + +  RGD  S  G+ + L +DP H  LFD
Sbjct: 290 RVDLTESLGGVSYAHLIGPDGEKIIVEERGDHRSSDGDMVDLVVDPDHMFLFD 342


Lambda     K      H
   0.319    0.137    0.387 

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: 394
Number of extensions: 14
Number of successful extensions: 3
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: 367
Length of database: 350
Length adjustment: 29
Effective length of query: 338
Effective length of database: 321
Effective search space:   108498
Effective search space used:   108498
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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