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.
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:
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