GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deh in Paraburkholderia bryophila 376MFSha3.1

Align The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) (characterized)
to candidate H281DRAFT_01646 H281DRAFT_01646 Nitrate/nitrite transporter

Query= TCDB::Q7X4L6
         (552 letters)



>FitnessBrowser__Burk376:H281DRAFT_01646
          Length = 465

 Score =  219 bits (558), Expect = 2e-61
 Identities = 125/330 (37%), Positives = 185/330 (56%), Gaps = 12/330 (3%)

Query: 10  PAPIT-SEERRVIFASSLGTVFEWYDFYLAGSLAIYI-SRTFFS-GVNPAAGFVFTLLGF 66
           P P T S  RR +  + LG + EWYDF+L G+ A  +  + FF  G +P  G +    GF
Sbjct: 32  PVPRTRSAARRAVTTAVLGQILEWYDFFLYGTAAALVFGKLFFPVGSDPLTGTIAAFGGF 91

Query: 67  AAGFAVRPFGAIVFGRLGDMIGRKYTFLATILLMGLSTFVVGLLPGYGTIGMTAPVVFIA 126
             GF  RP G ++ G +GD  GRK   + T+L MG +T ++G+LP Y  IG+ APV+ + 
Sbjct: 92  TVGFIARPIGGVLCGHIGDRYGRKVVMMLTLLTMGSATALMGVLPTYQQIGIAAPVMLVL 151

Query: 127 MRMLQGLALGGEYGGAATYVAEHAPSNKRGAWTAWIQTTATLGLFISLLVILSVRSLLNE 186
           +R++QGLA GGE+ G+   + E+AP +KRGA  AW    A LG  +S    L V++L + 
Sbjct: 152 LRIMQGLAAGGEWSGSILLIHENAPQSKRGALAAWSPCGAALGFVLSTGAFLLVQNLSST 211

Query: 187 DTFAAWGWRVPFLVSIVLLAVSVWIRMQLHESPVFERIKAEGKTSKAPLSEAFGQWKNLK 246
           D F +WGWR+PFL S  L+ + +W+R  + ES  F  +KA    S+ P+ E     K   
Sbjct: 212 D-FQSWGWRLPFLGSTALVVLGLWMRRSVGESAAFAEVKATRHQSRMPVIEVL---KQCP 267

Query: 247 IVLLALFGLTAGQAVVWYTGQFYTLFFLTQTLKVDGTSANML--VAVALLIGTPFFLFFG 304
             +L +FGL  G+    Y    +  F L     V   SA +L  + +++L+  P  LFFG
Sbjct: 268 REVLTVFGLRFGEGAASY---IFFAFSLAYGQFVGIKSAWVLSGLTISMLLMIPVTLFFG 324

Query: 305 SLSDKIGRKPIIMAGCLIAALTYFPLFKAL 334
            ++DK+GRKP+ +AG +   L  +P F  L
Sbjct: 325 HVTDKVGRKPVYLAGAIAIVLVAWPYFVLL 354



 Score = 34.3 bits (77), Expect = 1e-05
 Identities = 22/93 (23%), Positives = 42/93 (45%), Gaps = 1/93 (1%)

Query: 451 WPMSILILTILVLYVTMVYGPLAAMLVEMFPARIRYTSMSLPYHIGNGWFGGFLPATAFA 510
           W + + ++    + + M+ G   A + EM P  +R++ + +   + +   GG  P  A A
Sbjct: 360 WKVLVALILANSITLGMLEGAQPAFISEMLPVHLRFSGLGIGREVSSVLGGGLSPMIATA 419

Query: 511 IIAARGNIYSGLWYPIVIASVAFVIGTLFVKET 543
           ++A   +      Y   +  V  VI TL  +ET
Sbjct: 420 LLAHYRSALPVALYLGALGLVT-VIATLLARET 451



 Score = 30.0 bits (66), Expect = 2e-04
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 78  IVFGRLGDMIGRKYTFLATILLMGLSTFVVGLLPGYGTIGMTAPVVFIAMRMLQGLALGG 137
           + FG + D +GRK  +LA  + + L  +   +L G G        V +A+ +   + LG 
Sbjct: 321 LFFGHVTDKVGRKPVYLAGAIAIVLVAWPYFVLLGSGEYWK----VLVALILANSITLGM 376

Query: 138 EYGGAATYVAEHAPSNKR 155
             G    +++E  P + R
Sbjct: 377 LEGAQPAFISEMLPVHLR 394


Lambda     K      H
   0.325    0.139    0.420 

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: 625
Number of extensions: 27
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 552
Length of database: 465
Length adjustment: 34
Effective length of query: 518
Effective length of database: 431
Effective search space:   223258
Effective search space used:   223258
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: 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