Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_092344168.1 BLU87_RS01535 TRAP transporter large permease
Query= uniprot:I7DRS6 (467 letters) >NCBI__GCF_900107645.1:WP_092344168.1 Length = 429 Score = 218 bits (555), Expect = 3e-61 Identities = 139/457 (30%), Positives = 220/457 (48%), Gaps = 49/457 (10%) Query: 13 LLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFT---LLAIPFFILASSF 69 +LL+G P V L S L+L IY + T+ + T L+ +P FIL+++ Sbjct: 11 MLLLGFPFMVTLLGSIVLYLFIYMPDFAPKMLITMVQQVITGVTPPALVCVPMFILSANI 70 Query: 70 MTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGSIVIAGMRQ 129 +T+G A R+I VGHL GGL I +C LF A+SGS+ ATV AIG + + + Sbjct: 71 ITSGESAGRLIHMLKVFVGHLHGGLPITTNASCTLFGAVSGSTQATVAAIGGTMRPMLLE 130 Query: 130 VGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLMAGLMLMVT 189 GY F G+I N+ + LIPPSI +VY A S+G +FLAG++PGLM LM Sbjct: 131 AGYKSSFTLGLIINSSDIAFLIPPSIGFIVYGVATSTSIGSLFLAGILPGLMILLMFSTY 190 Query: 190 IYVMA---KVKNLPKGEWLGWGEVAASAANASVGLLLIG---IILGGIYGGIFTPTEAAA 243 Y + K+K LPK W A GL ++G II+GGIY G+F PTEAAA Sbjct: 191 CYFYSRFKKIKTLPKASW------AERRKAIKDGLPVLGFPVIIVGGIYTGLFNPTEAAA 244 Query: 244 VASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTRHAL 303 A +YA + +Y+ + T I SF Sbjct: 245 AAVLYAIVLEAVIYKAI-------------------------TFNRLIDSF--------- 270 Query: 304 FEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLIGGQ 363 + G +T + ++ ++ Q+P ++ + + + +V V+ + Sbjct: 271 LQTGVITGVVFILVGAGQAFSFLIGFLQLPAKLLPPLFGPEPSQLWVITIVVVVYFVACM 330 Query: 364 FMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVAGMP 423 F++P + +++P+ P + G+DPI LG+++ + IG TPP G ++F + P Sbjct: 331 FVDPIVAIFVLSPVFKPYVLSAGVDPILLGVLVTLQAAIGSATPPFGCDIFTAQLIFRRP 390 Query: 424 MMAVVRAALPFLAVLFVFLIMITYIPWISTVLPNAVM 460 + V+ +LPFL +L + +++ P I+ LPN + Sbjct: 391 YLEVIGHSLPFLLILILATVILVAFPQIALFLPNIAL 427 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: 592 Number of extensions: 29 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 467 Length of database: 429 Length adjustment: 33 Effective length of query: 434 Effective length of database: 396 Effective search space: 171864 Effective search space used: 171864 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