GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Dechlorosoma suillum PS

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate Dsui_2943 Dsui_2943 ABC-type spermidine/putrescine transport system, ATPase component

Query= reanno::WCS417:GFF4321
         (386 letters)



>FitnessBrowser__PS:Dsui_2943
          Length = 356

 Score =  200 bits (509), Expect = 5e-56
 Identities = 136/370 (36%), Positives = 197/370 (53%), Gaps = 27/370 (7%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           MA LEL +V + YGA     +  I   I+ G    L+GPSGCGK+TL+ CIAG E I  G
Sbjct: 1   MAHLELADVMQRYGAHT--VVDGIGFHIEAGVIACLLGPSGCGKTTLLRCIAGFEDIAAG 58

Query: 61  AIMIGDQDVSG----MSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEV 116
           +I +  + VS     ++P+ R I MVFQ YAL+P ++V +NI FGLK +     +    V
Sbjct: 59  SIALDGELVSRPGFKLAPEQRRIGMVFQDYALFPHLTVADNIAFGLKTKG---GERQQRV 115

Query: 117 ARVAKLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176
           A +  L+ +     + P +LSGGQQQRVA+ RALA  P++ L DEP SNLD  LR  +  
Sbjct: 116 AAMLDLVGLAGQGEKYPHELSGGQQQRVALARALAPAPRLVLLDEPFSNLDVDLRERLSL 175

Query: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFI 236
           E++ + ++  TT + VTHDQ EA  + D++ VM +G IQQ+ TP  +Y+ PAN+FVA F+
Sbjct: 176 EVREILKKAGTTAILVTHDQHEAFAMADEIGVMHEGRIQQWDTPYNLYHQPANRFVADFV 235

Query: 237 GS----PPMNFVPLRLQRKDGRLVALLDSG-QARCELALNTTEAGLEDRDVILGLRPEQI 291
           G     P       R+Q + G    +L+SG    C         G     V + LRP+ +
Sbjct: 236 GQGVFVPGTVLAGNRVQMELG----ILESGVPVECSAGCGVCGKGC---GVDILLRPDDV 288

Query: 292 MLAAGEGDSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQ-VGETLTLQFD 350
           +      D  S ++A V+     G D L  ++L        L P      +GE + ++ D
Sbjct: 289 V-----HDDKSPLQAAVEHKAFRGADILYTLRLESGARVLSLVPSHHNHALGEKIGIRLD 343

Query: 351 PSKVLLFDAN 360
              V+ F  N
Sbjct: 344 VDHVVAFKQN 353


Lambda     K      H
   0.318    0.135    0.382 

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: 326
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: 386
Length of database: 356
Length adjustment: 30
Effective length of query: 356
Effective length of database: 326
Effective search space:   116056
Effective search space used:   116056
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