Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_086509695.1 BZY95_RS09470 TRAP transporter large permease
Query= uniprot:Q88NP0 (426 letters) >NCBI__GCF_002151265.1:WP_086509695.1 Length = 419 Score = 334 bits (856), Expect = 3e-96 Identities = 166/412 (40%), Positives = 272/412 (66%), Gaps = 4/412 (0%) Query: 10 FIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQVASGVNKFSLLAIPFFVLAGAIMA 69 F +L+G+P+A A+G S L+ +PL + Q+ G+N F+L+A+P F+LAG +MA Sbjct: 9 FFAFMLLGVPIALAIGASTLLALNAQGVPLMVVTQQMFQGINSFALVAVPMFILAGDLMA 68 Query: 70 EGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLIPEMERKG 129 +G +S +LV FA L GF++GGLSLV++ A FF AISGS A TA+VGS L+PE++RKG Sbjct: 69 QGKVSEKLVDFADSLFGFLKGGLSLVSVGAGMFFAAISGSGAATTAAVGSSLVPELKRKG 128 Query: 130 Y-PREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLLSAVMMG 188 Y P ++ + SG++ ++ PPS ++Y++ A +VS LF+ GI+PG+L+ + Sbjct: 129 YDPASAASLIAASGTIGVVI-PPSVPMIIYAVVAQQSVS--KLFLNGIVPGILMGIGLAA 185 Query: 189 LCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATESAAVAVVW 248 + + A +RNYP+G + L + A WGLM VIILGGI SG+FT +E+A VAV + Sbjct: 186 IAITQAYRRNYPRGTALSLATIWRTFKSASWGLMTPVIILGGIFSGIFTPSEAAVVAVNY 245 Query: 249 SFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSKITTAFLT 308 + V++F+YRD D+ +++ R+ T +++M++I +A + ++ Q+P I L+ Sbjct: 246 ALLVSLFVYRDLSLGDVYRILIRSAITTAVIMLVIATSAVLSWTLSSWQVPGTIAQTVLS 305 Query: 309 LSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMIMLVNLGI 368 LS N YVI++ I +++L G ++ A ++ILTP+LLP++ +G+DP+HFG+I+++ L I Sbjct: 306 LSTNPYVIMLLIVAVILLTGVFIETASALIILTPVLLPLVLQLGIDPIHFGIIIVMGLAI 365 Query: 369 GLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLW 420 G+ITPPV L+V S++ ++ +E +A++P+ L L VL+ V Y+P + W Sbjct: 366 GMITPPVAINLYVASSVTQLPLERITRAILPYLLGLIGVLLLVVYVPIMLGW 417 Lambda K H 0.329 0.142 0.418 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: 531 Number of extensions: 27 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: 426 Length of database: 419 Length adjustment: 32 Effective length of query: 394 Effective length of database: 387 Effective search space: 152478 Effective search space used: 152478 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: 50 (23.9 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