GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Marinobacter adhaerens HP15

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 GFF2209 HP15_2163 sugar ABC transporter, ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__Marino:GFF2209
          Length = 366

 Score =  207 bits (527), Expect = 4e-58
 Identities = 125/343 (36%), Positives = 189/343 (55%), Gaps = 18/343 (5%)

Query: 19  YSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKLMNDASPKDRD 78
           Y++   +   H       +GPSGCGKST L +I+GL   +EG++  D K +N+ SP+DR+
Sbjct: 23  YAIRQLDHVWHKGGAYALLGPSGCGKSTMLNIISGLVQPSEGDVLFDGKRVNELSPRDRN 82

Query: 79  IAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEILGLTEFLERKPADLSG 138
           IA VFQ   +Y  M+VY+N+AF LK  K     I  RVHE AE+L + + L +K  +L+ 
Sbjct: 83  IAQVFQFPVIYDSMTVYDNLAFPLKNNKVPASKIKARVHEIAEVLEIEDKLYKKAKNLTA 142

Query: 139 GQRQRVAMGRAIVR-DAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTIYVTHDQT 197
            ++Q+V+MGR +VR D    L DEPL+ +D +L+  +R ++ +IH +   T +YVTHDQ 
Sbjct: 143 DEKQKVSMGRGLVREDVSAILFDEPLTVIDPQLKWKLRRKLKQIHEQFDITMVYVTHDQL 202

Query: 198 EAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVAGFIGSPAMNFFEVT 257
           EA T AD+I +M            G+I Q GTP EL+ +P + FV  FIGSP MN  EV 
Sbjct: 203 EASTFADKIAVMYG----------GQIVQFGTPTELFEQPNHTFVGFFIGSPGMNLIEVQ 252

Query: 258 VEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDISSDQIVHETFPNASVTA 317
               R V      ++L   Q  +L+        + +GIRPE +    +  +     +  A
Sbjct: 253 -RCPRGVCFGSTVVSLESWQVDVLQRT--RSTNIKIGIRPEFVEVSSVASDD----TFEA 305

Query: 318 DILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQLTF 360
           ++L  E LG+  ++ V+    +   R +   + S G KV L+F
Sbjct: 306 EVLDVEDLGTYKIVTVQLDHEKMKVRQSEEFAASIGSKVHLSF 348


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: 331
Number of extensions: 12
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: 366
Length adjustment: 30
Effective length of query: 347
Effective length of database: 336
Effective search space:   116592
Effective search space used:   116592
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 17 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