GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deh in Herbaspirillum seropedicae SmR1

Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate HSERO_RS11125 HSERO_RS11125 major facilitator transporter

Query= TCDB::F8SVK1
         (552 letters)



>FitnessBrowser__HerbieS:HSERO_RS11125
          Length = 553

 Score =  814 bits (2103), Expect = 0.0
 Identities = 398/552 (72%), Positives = 461/552 (83%), Gaps = 3/552 (0%)

Query: 1   MATVSGQISHAPMTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFI 60
           M T S   +   +T EEK+VIFASSLGTVFEWYDFYL GSLAA I+K FF+G +P  AFI
Sbjct: 1   MTTASVNTTARGITPEEKKVIFASSLGTVFEWYDFYLYGSLAAIIAKQFFAGTDPNTAFI 60

Query: 61  FTLLGFAAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMAS 120
           F LL FAAGF VRPFGALVFGRLGD+VGRKYTFL+TI+IMG ST +VG LP Y +IG+ +
Sbjct: 61  FALLAFAAGFIVRPFGALVFGRLGDLVGRKYTFLVTILIMGASTFIVGVLPNYNSIGITA 120

Query: 121 PVIFIAMRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGV 180
           P+I I +R+LQGLALGGEYGGAATYVAEHAP  RRG +TAWIQTTAT+GLFLSLLVILGV
Sbjct: 121 PIILIILRILQGLALGGEYGGAATYVAEHAPEGRRGSFTAWIQTTATMGLFLSLLVILGV 180

Query: 181 RTAMGEDAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFG 240
           RTA+GE AF  WGWRIPF+ S++LL ISVWIRM ++ESPAF ++KAEGKTSKAPL+EAFG
Sbjct: 181 RTAVGEAAFADWGWRIPFLVSILLLAISVWIRMSMNESPAFLKMKAEGKTSKAPLTEAFG 240

Query: 241 QWKNLKIVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFF 300
           QWKNLK+VILAL+G+TAGQAVVWYTGQFYALFFLTQTLKVDG +ANILIA ALL+ TPFF
Sbjct: 241 QWKNLKLVILALVGLTAGQAVVWYTGQFYALFFLTQTLKVDGPTANILIAAALLLATPFF 300

Query: 301 LFFGSLSDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDEC 360
           LFFGSLSD+IGRKPIIL GCLIAA+TYFP+F  LTH+ANPALEAA QKSP++V A+P  C
Sbjct: 301 LFFGSLSDKIGRKPIILGGCLIAAVTYFPIFSGLTHFANPALEAALQKSPVIVTADPASC 360

Query: 361 SFQFNPVGTSKFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYDGKAADA 420
            FQFNP GT KFTSSCDI K+ LS A +NY NVA   G++A +K+GD  I +YD      
Sbjct: 361 QFQFNPTGTKKFTSSCDIVKAKLSAASVNYQNVAGAPGSVATVKIGDRIITSYDAAGLSK 420

Query: 421 KDAG---KAFDKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLV 477
           +DA    K   K+L   +KAA YP KADP Q+N PM +++L ILVIYVTMVYGPIAA LV
Sbjct: 421 EDAAAKDKQLSKDLADDIKAAGYPSKADPEQMNKPMVLLLLFILVIYVTMVYGPIAACLV 480

Query: 478 EMFPTRIRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGL 537
           EMFPTRIRYTSMS+PYHIGNGWFGG LP T+FA+VA KG+IY GLWYPI+IA+ TFVIG+
Sbjct: 481 EMFPTRIRYTSMSMPYHIGNGWFGGLLPTTSFALVAFKGDIYYGLWYPIVIAMITFVIGM 540

Query: 538 LFVRETKDSNIY 549
           LFV+ET  +NI+
Sbjct: 541 LFVKETVRNNIH 552


Lambda     K      H
   0.325    0.139    0.422 

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: 926
Number of extensions: 36
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: 552
Length of database: 553
Length adjustment: 36
Effective length of query: 516
Effective length of database: 517
Effective search space:   266772
Effective search space used:   266772
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 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