Align The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) (characterized)
to candidate WP_057507667.1 ABB28_RS05485 proline/glycine betaine transporter ProP
Query= TCDB::Q7X4L6 (552 letters) >NCBI__GCF_001431535.1:WP_057507667.1 Length = 495 Score = 202 bits (514), Expect = 2e-56 Identities = 111/313 (35%), Positives = 167/313 (53%), Gaps = 2/313 (0%) Query: 18 RRVIFASSLGTVFEWYDFYLAGSLAIYISRTFFSGVNPAAGFVFTLLGFAAGFAVRPFGA 77 RR + A++LG EW+DF + G LA+ + + FF NP A + T F F VRP G Sbjct: 34 RRAVGAAALGNAMEWFDFGVYGYLAVTLGQVFFPASNPTAQLIATFATFTVAFLVRPLGG 93 Query: 78 IVFGRLGDMIGRKYTFLATILLMGLSTFVVGLLPGYGTIGMTAPVVFIAMRMLQGLALGG 137 +VFG LGD GR+ T++LM L TF +GL+P Y IG+ APV+ + R++QG + GG Sbjct: 94 LVFGPLGDRYGRQKVLAFTMILMALGTFSIGLIPSYERIGIWAPVLLLLARLVQGFSTGG 153 Query: 138 EYGGAATYVAEHAPSNKRGAWTAWIQTTATLGLFISLLVILSVRSLLNEDTFAAWGWRVP 197 EYGGAAT++AE+A RG +W++ G + ++ LL+ WGWR+P Sbjct: 154 EYGGAATFIAEYATDRNRGLMGSWLEFGTLGGYIAGAATVTTLHLLLSGAQMLDWGWRIP 213 Query: 198 FLVSIVLLAVSVWIRMQLHESPVFERIKAEGKTSKAPLSEAFGQWKNLK-IVLLALFGLT 256 FLV+ L + +++RM+L E+P F R AE + G+ + LL GL Sbjct: 214 FLVAGPLGLLGLYMRMRLEETPAF-RAYAEEAAKRDHERPGLGELLRVHGRQLLICMGLV 272 Query: 257 AGQAVVWYTGQFYTLFFLTQTLKVDGTSANMLVAVALLIGTPFFLFFGSLSDKIGRKPII 316 V Y Y +LT TL + +L+ + +L+ P + G SD++GR+P+I Sbjct: 273 LVFNVTDYMLLTYMPSYLTVTLGYAESKGLLLIIIVMLVMMPLNIVGGLFSDRLGRRPMI 332 Query: 317 MAGCLIAALTYFP 329 + C+ L P Sbjct: 333 IGACIALLLLAIP 345 Score = 37.4 bits (85), Expect = 1e-06 Identities = 22/93 (23%), Positives = 50/93 (53%), Gaps = 3/93 (3%) Query: 455 ILILTILVLYVTMVY--GPLAAMLVEMFPARIRYTSMSLPYHIGNGWFGGFLPATAFAII 512 ++ L +++L + +V + + L +F +RY+++S+ +++ FGG P ++ Sbjct: 357 LIFLGLMLLGIALVCFTSSMPSTLPALFYTPVRYSALSIAFNVSVSLFGGTTPLVTAWLV 416 Query: 513 AARGNIYSGLWYPIVIASVAFVIGTLFVKETKG 545 G+ +Y ++ A+V ++ LFV+ET G Sbjct: 417 ERSGDPMVPAYY-LMGAAVIGLVTMLFVRETAG 448 Score = 25.0 bits (53), Expect = 0.007 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 6/64 (9%) Query: 291 VALLIGTPFFLFFGSLSDKIGRKPIIMAGCLIAALTYFPLFKALAHYTNPKLEAATLQAP 350 VA L+ L FG L D+ GR+ ++ ++ AL F + P E + AP Sbjct: 84 VAFLVRPLGGLVFGPLGDRYGRQKVLAFTMILMALGTFSIGLI------PSYERIGIWAP 137 Query: 351 ITMI 354 + ++ Sbjct: 138 VLLL 141 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: 605 Number of extensions: 28 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 3 Length of query: 552 Length of database: 495 Length adjustment: 35 Effective length of query: 517 Effective length of database: 460 Effective search space: 237820 Effective search space used: 237820 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 24 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