Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate 3607682 Dshi_1091 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= reanno::SB2B:6938090 (466 letters) >FitnessBrowser__Dino:3607682 Length = 424 Score = 259 bits (661), Expect = 2e-73 Identities = 163/457 (35%), Positives = 249/457 (54%), Gaps = 37/457 (8%) Query: 1 MTIATLFLTLFLCMLLGMPIAIALGFSSMLTILLFSNDSLASVALKLYEATSEHYTLLAI 60 MTI + + LF+ +LLG+P+A ALG + ++L L +A + +T + + LLA+ Sbjct: 1 MTIILILVALFVLLLLGVPVAFALGGMGLAMLILGGFSPL--MAPQSILSTLDGFILLAV 58 Query: 61 PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120 P F+L S L GGV R + VGH GGLA+A++++C LFAA+SGSS AT A IG Sbjct: 59 PLFLLMSNLLLKGGVGRDLFAAVQAWVGHWPGGLAVATILSCALFAAISGSSVATAATIG 118 Query: 121 SIVIVGMVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGL 180 ++ I M+ GY +KF G++ GTLGILIPPSI M+VY TE S +F+AG+ PGL Sbjct: 119 TVAIPEMINRGYEKKFVYGLLAAGGTLGILIPPSIPMIVYGFVTEQSVIALFLAGIGPGL 178 Query: 181 LMGVLLMVAIYIVARIKNLPSRPFPGVKALSLSSAK-AMGGLALIFIVLGSIYGGVASPT 239 L+ L ++ + AR+ + A +S++K A+ +AL +V+ +Y G +PT Sbjct: 179 LLVTLFVLFAMLHARLSGTYTPVPKATMAERMSASKRALPSVALAALVIVGLYSGAFTPT 238 Query: 240 EAAAVACVYAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHVGLGLIKTPTDKEI 299 EAAA+ G A AIV L +T T Sbjct: 239 EAAAI---------------------------GSAAALAIVTLWL-------RTLTWVTF 264 Query: 300 RNVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWGFLIIVNLLLL 359 VR+ A + +L I+A A +F + RIP I+ + P F+++V+L+LL Sbjct: 265 WEAVRESAITTAAILLIVAGAKVFGKAIALYRIPQDISAFLTQVIDGPIMFIVVVSLVLL 324 Query: 360 AAGNFMEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGI 419 G E +++LIM P+L P A+ LG DPI GI MV+ +E ++TPPVGLNL+V + Sbjct: 325 LMGLVFEALSMILIMTPVLLPAAMGLGFDPIWFGIYMVIMVECALITPPVGLNLYVIQSV 384 Query: 420 TGRSIGWVIHACLPWLLLLLGFLVLITYVPQISLFLP 456 ++ V P+L+L+L + ++ PQ++L++P Sbjct: 385 ARTTLSNVARGVWPFLILMLVTVGVLYAFPQLALYIP 421 Lambda K H 0.329 0.144 0.424 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: 591 Number of extensions: 33 Number of successful extensions: 6 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: 466 Length of database: 424 Length adjustment: 32 Effective length of query: 434 Effective length of database: 392 Effective search space: 170128 Effective search space used: 170128 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 17 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