GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Dinoroseobacter shibae DFL-12

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 3608624 Dshi_2017 ABC transporter related (RefSeq)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>FitnessBrowser__Dino:3608624
          Length = 333

 Score =  309 bits (791), Expect = 8e-89
 Identities = 171/367 (46%), Positives = 230/367 (62%), Gaps = 36/367 (9%)

Query: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60
           MATL L NV K++G    D +  + + + +GEF+++VGPSGCGKSTL+  +AGLET+S G
Sbjct: 1   MATLTLDNVKKSFGK--TDVIHGVSIDVTEGEFIVIVGPSGCGKSTLLRMVAGLETVSSG 58

Query: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120
            + +D   ++ + P DRDIAMVFQ+YALYP MSV DN+A+GLKI K+P AEI + VA  +
Sbjct: 59  EVRIDGRVVNTLEPMDRDIAMVFQNYALYPHMSVFDNMAYGLKIAKVPKAEIADRVAVAA 118

Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           KLLQ+E  L RKP +LSGGQ+QRVAMGRA+ R+P ++LFDEPLSNLDAKLRV+MR E+K 
Sbjct: 119 KLLQLEPYLGRKPKELSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEIKA 178

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240
           + + L  T++YVTHDQ+EAMTL D++ VM  G+  Q G P ++Y NP   FVA FIGSPP
Sbjct: 179 LQRELGVTSLYVTHDQVEAMTLADRMIVMNGGVADQIGAPLEVYANPQTAFVAGFIGSPP 238

Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANG 300
            NF+P  + R                  P G Q          +GIRPE + +A      
Sbjct: 239 TNFLPADMVRAG----------------PAGQQ----------VGIRPEHLRVA-----P 267

Query: 301 LPTIRAEVQVTEPTGPDTLVFVNLND--TKVCCRLAPDVAPAVGETLTLQFDPAKVLLFD 358
              + A V   E  G +TL+ +  +   T    + A    PA G T+ L +D +  +LF 
Sbjct: 268 QGRLEAHVAYAEALGAETLLHLRASQGTTLTVRQDAAAPMPAEGATVQLDWDDSDTMLF- 326

Query: 359 AKTGERL 365
           A  G R+
Sbjct: 327 ADNGRRV 333


Lambda     K      H
   0.319    0.138    0.393 

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: 382
Number of extensions: 17
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: 386
Length of database: 333
Length adjustment: 29
Effective length of query: 357
Effective length of database: 304
Effective search space:   108528
Effective search space used:   108528
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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