GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_085637869.1 MGEO_RS12095 ABC transporter ATP-binding protein

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



>NCBI__GCF_002115805.1:WP_085637869.1
          Length = 365

 Score =  345 bits (884), Expect = 2e-99
 Identities = 191/362 (52%), Positives = 242/362 (66%), Gaps = 10/362 (2%)

Query: 4   LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63
           LE+RN+ K++G    D LKNI + ID G+F++LVGPSGCGKSTL+NCIAGLE I+ G I 
Sbjct: 5   LEIRNLYKSFGS--VDVLKNINVSIDPGDFVVLVGPSGCGKSTLLNCIAGLEPITRGTIE 62

Query: 64  VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123
           +   D++ +  +DRDIAMVFQSYALYPTMSV  NI FG+++R +     ++++A V++LL
Sbjct: 63  IAGEDMTDVPARDRDIAMVFQSYALYPTMSVAQNITFGMRVRGIDRETREKKLAEVARLL 122

Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
           +IE LL R+P QLSGGQ+QRVAMGRAL R PK++LFDEPLSNLDAKLRVEMR E++ +HQ
Sbjct: 123 KIEPLLDRRPKQLSGGQRQRVAMGRALVREPKLFLFDEPLSNLDAKLRVEMRAEIRRLHQ 182

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243
           RL TT VYVTHDQIEAMTL  K+AVMK G + Q G PK+IY  P N+FVA FIGSP MN 
Sbjct: 183 RLSTTIVYVTHDQIEAMTLATKIAVMKAGEVHQIGKPKEIYERPVNMFVADFIGSPSMNL 242

Query: 244 IPLRLQRKDGRL-LALLDSGQARCELPLGMQDAGLED--REVILGIRPEQIILANGEANG 300
            P R  R DG   L +  SG A    PL ++D    D   +V++G+RPE I  AN  +  
Sbjct: 243 FPARATRVDGHTRLEVSRSGGA----PLVLKDPRQFDLPSQVVVGLRPEDIAEANLRSGP 298

Query: 301 -LPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDA 359
            + T    +   E +G DT V   L    V  R   +     G  +   FD AKVL F  
Sbjct: 299 FVQTGTCRIDFIEQSGSDTYVLTKLGGVDVFGRFHTETHVEEGMEIDFAFDLAKVLFFHP 358

Query: 360 KT 361
           +T
Sbjct: 359 ET 360


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: 419
Number of extensions: 23
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: 386
Length of database: 365
Length adjustment: 30
Effective length of query: 356
Effective length of database: 335
Effective search space:   119260
Effective search space used:   119260
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: 50 (23.9 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