GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lysL in Sinorhizobium meliloti 1021

Align L-lysine transport protein (characterized)
to candidate SMa1667 SMa1667 ArcD1 arginine/ornithine antiporter

Query= CharProtDB::CH_019644
         (501 letters)



>lcl|FitnessBrowser__Smeli:SMa1667 SMa1667 ArcD1 arginine/ornithine
           antiporter
          Length = 475

 Score =  360 bits (924), Expect = e-104
 Identities = 201/489 (41%), Positives = 291/489 (59%), Gaps = 18/489 (3%)

Query: 15  ATSRTVSIRTLIALIIGSTVGAGIFSIPQNIGSVAGPGAMLIGWLIAGVGMLSVAFVFHV 74
           +T++ +S+ +L AL++GS VGAGIFS+P+  G   GP   ++ W IAG G+ ++A VF V
Sbjct: 3   STAQKLSLASLAALVVGSMVGAGIFSLPRTFGDATGPFGAIVAWCIAGAGIFTLAHVFRV 62

Query: 75  LARRKPHLDSGVYAYARVGLGDYVGFSSAWGYWLGSVIAQVGYATLFFSTLGHYVPLFSQ 134
           LA RK  LD+GVYAYA  G GDY GF S  GYWL   IA V Y  L  +TLG + P+F  
Sbjct: 63  LAERKSDLDAGVYAYANAGFGDYAGFLSVLGYWLVGCIADVSYWVLIKATLGAFFPIFGD 122

Query: 135 DHPFVSALAVSALTWLVFGVVSRGISQAAFLTTVTTVAKILPLLCFIILVAFLG-FSWEK 193
            +   + L  S   W    ++ RGI +AA + TV TVAKI+P+L FI+++  LG F  + 
Sbjct: 123 GNTIAAVLVSSVALWGFHFMILRGIKEAAAINTVVTVAKIVPILIFIVIL--LGAFETDL 180

Query: 194 FTVDLWA-RDGGVGSIFDQVRGIMVYTVWVFIGIEGASVYSRQARSRSDVSRATVIGFVA 252
           F  + W   D    S+F+Q+R  M+ TV+VFIG+EGASVYSR AR RSDV  AT +GFV 
Sbjct: 181 FRSNFWGGADMPEASLFEQIRATMLVTVFVFIGVEGASVYSRYARKRSDVGVATTLGFVV 240

Query: 253 VLLLLVSISSLSFGVLTQQELAALPDNSMASVLEAVVGPWGAALISLGLCLSVLGAYVSW 312
           VL L+V ++ L +G L + E+AA+   SMASVLE++VGPWG+  +S GL +SVLGAY++W
Sbjct: 241 VLGLMVLVTLLPYGALERPEIAAMRQPSMASVLESIVGPWGSVFVSAGLIVSVLGAYLAW 300

Query: 313 QMLCAEPLALMAMDGLIPSKIGAINSRGAAWMAQLISTIVIQIFIIIFFLNETTYVSMVQ 372
            ++C E L   A +G +PS +   NS      A  +S  VIQ+F+I    +E  +  MV 
Sbjct: 301 SLICVEVLFCAAKNGDMPSVLARENSNSVPAAALWLSNGVIQLFLISTLFSEDAFRLMVN 360

Query: 373 LATNLYLVPYLFSAFYLVMLATRGKGITHPHAGTRFDDSGPEISRRENRKHLIVGLVATV 432
           L + + L+PYL  A Y  ++A RG+                 I  +E  + LI+   ATV
Sbjct: 361 LTSAMVLIPYLLVAAYGFLVAKRGETY--------------NIRPKERFRDLILAGAATV 406

Query: 433 YSVWLFYAAEPQFVLFGAMAMLPGLIPYVWTRIYRGEQVFNRFEIGVVVVLVVAASAGVI 492
           Y+ ++ YA   +F+L  A+    G   + + R  + + +F+  E  V + +V     G+ 
Sbjct: 407 YTAFMIYAGGLKFLLLSAILYALGTALFFYARREQKKPLFSPREWLVFIAVVAGCLVGIY 466

Query: 493 GLVNGSLSL 501
           GLV GS+++
Sbjct: 467 GLVTGSITI 475


Lambda     K      H
   0.327    0.139    0.421 

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: 667
Number of extensions: 35
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: 501
Length of database: 475
Length adjustment: 34
Effective length of query: 467
Effective length of database: 441
Effective search space:   205947
Effective search space used:   205947
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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