Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_045584776.1 AL072_RS30790 TRAP transporter large permease subunit
Query= uniprot:I7DRS6 (467 letters) >NCBI__GCF_001305595.1:WP_045584776.1 Length = 427 Score = 259 bits (661), Expect = 2e-73 Identities = 151/454 (33%), Positives = 246/454 (54%), Gaps = 37/454 (8%) Query: 6 LFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAIPFFIL 65 + ++++ LL+ G+PI ALGL+S L ++ + S+ S+A ++F + L IP F Sbjct: 5 ILALLLVLLMSGMPIFAALGLTSLGVLALF-EGSIDSMADSVFASLNNPL-LATIPMFAF 62 Query: 66 ASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGSIVIA 125 + M V + S VGH+ GGL+ A + +C +F+ +SGSS AT + IGSI I Sbjct: 63 MAHVMIKAKVVDDLYEMSNTLVGHIKGGLSFATILSCTIFSTISGSSVATALTIGSISIP 122 Query: 126 GMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLMAGLM 185 M++ GY + G+I GTLGILIPPS M++YA + S+G +FLAG+IPGL+ ++ Sbjct: 123 QMKRYGYRQRDTYGLIAAGGTLGILIPPSGPMILYAIVTDASIGALFLAGIIPGLLMAVV 182 Query: 186 LMVTIYVMAKVKNLPKGE-WLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTEAAAV 244 ++ AK ++ + + W G+G VAA+ + +L+ +ILGGIY G+FT EAAAV Sbjct: 183 FAGYSWLQAKRQDGVRSQSWPGFGAVAAAFRKSIWAVLMPPLILGGIYLGVFTAGEAAAV 242 Query: 245 ASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTRHALF 304 +VYA VA VYR++ AD Sbjct: 243 GAVYALAVALLVYRNLSV----------------------------------ADLLDCGV 268 Query: 305 EAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLIGGQF 364 + + + L +IA A + H +T ++P QI + + G F++ V + I G F Sbjct: 269 QTMRTSAMLFMIIAAAGMFGHAITIIRLPAQIMETVTALGLSQGGFILAVMAAIFILGMF 328 Query: 365 MEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVAGMPM 424 +E +++I P++ P+ LGI+P+ G+++++N+E+ +ITPPVG+NLFV G+ + Sbjct: 329 LETIAIILITTPIILPVMAALGINPVWYGVMLMINLELALITPPVGMNLFVIKGITNSSL 388 Query: 425 MAVVRAALPFLAVLFVFLIMITYIPWISTVLPNA 458 V R ALP++ ++ L ++ P +S LP A Sbjct: 389 GEVTRGALPYVLLMMAGLFIVWLFPALSLWLPQA 422 Lambda K H 0.329 0.144 0.421 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: 588 Number of extensions: 39 Number of successful extensions: 4 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: 467 Length of database: 427 Length adjustment: 33 Effective length of query: 434 Effective length of database: 394 Effective search space: 170996 Effective search space used: 170996 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