Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_004309484.1 C665_RS11110 C4-dicarboxylate ABC transporter permease
Query= SwissProt::O07838 (440 letters) >NCBI__GCF_000310185.1:WP_004309484.1 Length = 432 Score = 216 bits (551), Expect = 9e-61 Identities = 135/441 (30%), Positives = 229/441 (51%), Gaps = 23/441 (5%) Query: 1 MSALIIFGLLIALMLTGMPISISL-GLTVLTFLFTMTQVPIDTVALKLFTGIEKFEIMAI 59 M A ++ GL++AL+ G+ I ++L + +L L + P D +A+ +++ + + A+ Sbjct: 4 MIAAVLIGLMLALLAGGVWIGLALMAIGILGMLGFTPRAPGDGMAVAIWSHGSSWTLTAL 63 Query: 60 PFFILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIG 119 P F+ G L +++ M + + G L +I C LFAAVSGSS AT IG Sbjct: 64 PLFLWMGEILFRTKLSEDMFKGLSPWLERLPGRLLHTNIIGCTLFAAVSGSSAATCATIG 123 Query: 120 SVILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSA 179 + LP + +G+P+ G + +G LG+LIPPSI+M++Y VA + Sbjct: 124 KIALPELQRRGYPESMALGTLAGAGTLGLLIPPSIIMIVYGVA--------------ADV 169 Query: 180 SVGELFMAGVVPGLMLAGFLAFTTWNRARKFGYP-RLEKASLRQRWTAFREAAWGLMLIV 238 S+ +LF+ GV+PG++LA F W P ++ A L+ + A+ L+ ++ Sbjct: 170 SISKLFIGGVLPGILLASL--FMGWVVVWSLMNPGKIPAADLKTDFMGKLRASKNLIPVI 227 Query: 239 VVIGG----IYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLY 294 ++IGG IY+GI T TEAAA+ + + I+ + L + L+ + + M+ Sbjct: 228 LLIGGVLGSIYSGIATATEAAAIGVIGSLIIAAS-QRTLNRKSFFGALMGATRLYCMIAL 286 Query: 295 IITNAVLFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMA 354 I+ + + M + G+P+ L EW+ GL+ M L+ + I + G F++ SIV++ Sbjct: 287 ILAGSAFLTLAMGYIGLPRHLAEWIGGLGLTPGMLLVALAIFYILLGCFLDGISIVVLTM 346 Query: 355 PILFPVAVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWL 414 +L P GIDP+ FGI +VV +E+ PPVG NL+V G+T +T + P+ Sbjct: 347 AVLMPTIQAAGIDPLWFGIFVVVVVEMAQVTPPVGFNLFVLQGLTGRDMTVIARYALPYF 406 Query: 415 LTMLAFLVLVTYVPAISLALP 435 L M+ +VL+ P + LP Sbjct: 407 LLMVLAVVLLYTFPGLVTWLP 427 Lambda K H 0.329 0.142 0.431 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: 598 Number of extensions: 39 Number of successful extensions: 3 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: 440 Length of database: 432 Length adjustment: 32 Effective length of query: 408 Effective length of database: 400 Effective search space: 163200 Effective search space used: 163200 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: 51 (24.3 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