Align Large component of TRAP-type D-gluconate transporter (characterized)
to candidate GFF1297 PGA1_c13130 TRAP transporter, subunit DctM
Query= reanno::azobra:AZOBR_RS15920 (426 letters) >FitnessBrowser__Phaeo:GFF1297 Length = 491 Score = 221 bits (562), Expect = 5e-62 Identities = 152/479 (31%), Positives = 239/479 (49%), Gaps = 72/479 (15%) Query: 6 FLSSLFGLMLLGMPIAFALMLT-GVALMVHLDFFDAQLVAQNMLSGADNYPLMAVPFFIL 64 FL L+L+G+P+ F L+ G L ++ D L+ +N+ +G D++PLMA+PFF+L Sbjct: 5 FLPLFLFLLLIGLPVFFCLLAAPGALLWLNGQERDLTLLYRNLYNGMDSFPLMAIPFFML 64 Query: 65 AGELMNAGGISQRIINLAVSLVGHIRGGLGYVTIGASVMLASLSGSAIADTAALATLLIP 124 AGELMN GGI+ R++ + +L+GH+RGGL V I +S++ A LSGSA+ADT+AL ++LIP Sbjct: 65 AGELMNRGGITVRLVEFSQALMGHLRGGLAQVNILSSILFAGLSGSAVADTSALGSMLIP 124 Query: 125 MMRDNGYPVPRSAGLIASGGIIAPIIPPSMPFIIFGVTTNTSISGLFMAGIVPGLLMGAG 184 M GY +A + A+ +I PIIPPS II+ S++ LF+AGIVPG+L+G G Sbjct: 125 AMEREGYSRKFAAAVTAASSVIGPIIPPSGIMIIYAYVMGESVAALFLAGIVPGVLVGVG 184 Query: 185 LVITWMFVVRGMTVKLQPKAS----WGERRTALVEGVWALALPVIIIGGLRGGIFTPTEA 240 L M +VR M + + A+ + ++E ++ L + +G L E Sbjct: 185 L----MIMVRAMADRYELPAARRVVFDSVEIGVMERWFSFGLVRLNLGLLLAQFVPLAEG 240 Query: 241 A-----------VVAAVYSLVVALF-----VYRQVTLKDLVPL----------LVQAART 274 A V + L++ L +R + + +VPL L Sbjct: 241 AGAQMKWLAFFGAVLFAHGLMLGLRRVVSPAFRTICKRAVVPLQTPVLILGGILAGVFTP 300 Query: 275 TSTVMFLCAAALVSSYMV----TLADLPQ------------------------------- 299 T A AL+ S++V LADLPQ Sbjct: 301 TEAAAVAVAYALLISFLVLGSMRLADLPQVFSRAGITSAVVLLLVGAAMSFKTVVSLSHA 360 Query: 300 --QMNEMLAPLLHEPKLLMVAITLLLLAVGTVMDLTPTILVLGPVLTPLAAAAGIDPTYF 357 Q+ + + L P +L+ I LLL VG +D P I++LGP+L P+ G++ +F Sbjct: 361 PEQLADFILTLSENPLILLFLINLLLFVVGMFLDAGPAIIILGPILGPVFTDLGVESVHF 420 Query: 358 GVMFVLTGTLGLIHPPVCTVLNVVCGVARISLESATRGIWPFLLTYLLLLCLLIAVPEI 416 ++ + T+GL PP+ VL V V++ + + + I PFL + ++ L+ VP I Sbjct: 421 AIIMCVNLTVGLATPPMGLVLFVAAAVSQERVTTIAKAILPFLAIEIAVIFLITFVPAI 479 Lambda K H 0.328 0.142 0.420 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: 489 Number of extensions: 25 Number of successful extensions: 2 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: 491 Length adjustment: 33 Effective length of query: 393 Effective length of database: 458 Effective search space: 179994 Effective search space used: 179994 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