GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putP in Shewanella amazonensis SB2B

Align Osmoregulated proline transporter OpuE; Osmoprotectant uptake; Proline uptake system (characterized)
to candidate 6936303 Sama_0492 sodium/proline symporter (RefSeq)

Query= SwissProt::O06493
         (492 letters)



>FitnessBrowser__SB2B:6936303
          Length = 498

 Score =  557 bits (1435), Expect = e-163
 Identities = 278/496 (56%), Positives = 368/496 (74%), Gaps = 6/496 (1%)

Query: 1   MSIEIIISLGIYFIAMLLIGWYAFKKTTD-INDYMLGGRGLGPFVTALSAGAADMSGWML 59
           M     ISL +YFIAML IG +A++ +TD +  YMLGGR + P VTALSAGA+DMSGWML
Sbjct: 1   MEYSSYISLALYFIAMLAIGLFAYRNSTDDLAGYMLGGRQVSPHVTALSAGASDMSGWML 60

Query: 60  MGVPGAMFATGLSTLWLALGLTIGAYSNYLLLAPRLRAYTEAADDAITIPDFFDKRFQHS 119
           MG+PGAMF  G   LW+A GL +GA  NYLL+APRLR +TEAADDA+T+PDFF KRF   
Sbjct: 61  MGLPGAMFTMGYDALWIAAGLLLGALLNYLLVAPRLRVFTEAADDALTLPDFFSKRFNKD 120

Query: 120 SSLLKIVSALIIMIFFTLYTSSGMVSGGRLFESAFGADYKLGLFLTTAVVVLYTLFGGFL 179
           +  ++++SA +I++FFTLYTS+G+V+GG+ FESAFG  Y+ GL LT +VVV YTL GGFL
Sbjct: 121 NGSVRMISAAVIILFFTLYTSAGLVAGGKFFESAFGLGYQTGLLLTVSVVVAYTLLGGFL 180

Query: 180 AVSLTDFVQGAIMFAALVLVPIVAFTHVGGVAPTFHEIDAVNPHLLDIFKGASVISIISY 239
           AVSLTDFVQG IMF ALVLVP+VA            +       L D F+   +++I+S 
Sbjct: 181 AVSLTDFVQGCIMFLALVLVPLVALQEFNSSTDMLAQASRSITPLADSFEHMGILAIVSS 240

Query: 240 LAWGLGYYGQPHIIVRFMAIKDIKDLKPARRIGMSWMIITVLGSVLTGLIGVAYAHKFGV 299
           LAWGLGY+GQPHIIVRFMAI+ +KD+  AR IGMSWM++T+LG++ TGLIGVAY +KF  
Sbjct: 241 LAWGLGYFGQPHIIVRFMAIRSVKDIAVARNIGMSWMLVTILGALATGLIGVAYVNKFKP 300

Query: 300 AVKDPEMIFIIFSKILFHPLITGFLLSAILAAIMSSISSQLLVTASAVTEDLYRSFFRRK 359
            + D E IFI+F++ILFHPLI+GFLL+AILAAIMS+ISSQLLV++S+++ED+YR+ F ++
Sbjct: 301 GLDDGETIFILFAEILFHPLISGFLLAAILAAIMSTISSQLLVSSSSLSEDVYRALFHKE 360

Query: 360 ASDKELVMIGRLSVLVIAVIAVLLSLNPNSTILDLVGYAWAGFGSAFGPAILLSLYWKRM 419
              K  V  GR+ VL +A +A LL+L+ N++IL LV  AWAGFG+AFGP +LLSL+W RM
Sbjct: 361 MDQKATVTAGRIGVLAVAAVATLLALDNNASILSLVSNAWAGFGAAFGPLVLLSLFWPRM 420

Query: 420 NEWGALAAMIVGAATVLIW-----ITTGLAKSTGVYEIIPGFILSMIAGIIVSMITKRPA 474
              GA+A ++ GA TVL+W     +  GL  S+ +YEI+PGFI+S +A ++VS   + P 
Sbjct: 421 THSGAVAGILCGAGTVLVWSQVPLLENGLPLSSLIYEIVPGFIVSTLAIVLVSYADQAPC 480

Query: 475 KASYRLFGVMEKLLKR 490
           K++ + F +    LK+
Sbjct: 481 KSTQKAFKLSRDRLKQ 496


Lambda     K      H
   0.328    0.142    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: 743
Number of extensions: 38
Number of successful extensions: 5
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: 492
Length of database: 498
Length adjustment: 34
Effective length of query: 458
Effective length of database: 464
Effective search space:   212512
Effective search space used:   212512
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 (21.8 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:

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