Align Dicarboxylate (succinate, fumarate, malate) transporter, vcINDY (characterized)
to candidate BWI76_RS04380 BWI76_RS04380 anion transporter
Query= TCDB::Q9KNE0 (462 letters) >FitnessBrowser__Koxy:BWI76_RS04380 Length = 419 Score = 181 bits (459), Expect = 4e-50 Identities = 127/410 (30%), Positives = 214/410 (52%), Gaps = 22/410 (5%) Query: 45 VVLGISMLAFIAVLWLTEALHVTVTAILVPVMAVFFGIFETQAALNNFANSIIFLFLGGF 104 V + +S+L F V+++ E + + VTA++V + V G+F+ Q A + F N + LF+ F Sbjct: 4 VTITLSLLVFSIVMFVWEKIPLAVTAMIVCITLVVTGVFDVQTAFSGFINQNVILFVAMF 63 Query: 105 ALAAAMHHQGLDKVIADKVLAMAQGKMSVAVFMLFGVTALLSMWISNTATAAMMLPLVLG 164 + A+ G+ I V A+ + + V ++ V LLS +SNT TAA+++P+V+G Sbjct: 64 VVGGALFETGVTDKIGGIVTRYARSEKQLIVIIML-VCGLLSGVLSNTGTAAVLIPVVIG 122 Query: 165 VLSKVDADKQRSTYVFVLLGVAYSASIGGIATLVGSPPNAIAAA---EVGLSFT--DWMK 219 K + R +L+ +A+++++GG +L+GSP N IA + +VG SF ++ K Sbjct: 123 AAIKSGYARSR-----LLMPLAFASALGGNLSLIGSPGNLIAQSALEQVGQSFGFFEYAK 177 Query: 220 FGLPTAMMMLPMAIAILYFLL--KPTLNGMFELDRAPVNWDKGK-VVTLGIFGLTVFLWI 276 G+P + + I Y +L K TL V+ K V+ L + TV I Sbjct: 178 LGIPMLACGILYFVTIGYRILPGKNTLQKHGAESIRTVDCPTYKQVIALSVLIATVLGMI 237 Query: 277 FSSPINAALGGFKSFDTLVALGAILMLSFARVVHWKEIQKTADWGVLLLFGGGLCLSNVL 336 F I + + ++GA L L RV+ K+ + D + LFGG L L+ L Sbjct: 238 FEKRIGLPIA------IIGSIGA-LSLVMTRVITEKQAYQAIDSQTIFLFGGTLALAKAL 290 Query: 337 KQTGTSVFLANALSDMVSHMGI-FVVILVVATFVVFLTEFASNTASAALLIPVFATVAEA 395 + TG +A ++ D++ H F+++ V LT F SNTA+AALL+P+ ++A + Sbjct: 291 ETTGAGAIMARSIIDLLGHQASPFLLLSAVLIISCILTNFMSNTATAALLMPIGLSIAHS 350 Query: 396 FGMSPVLLSVLIAVAASCAFMLPVATPPNAIVFASGHIKQSEMMRVGLYL 445 G P + + I + SCA+ PV TP N ++F++G K + ++VGL L Sbjct: 351 MGADPRAVLMAIVIGCSCAYATPVGTPANMMIFSAGGYKFVDYVKVGLPL 400 Score = 64.7 bits (156), Expect = 6e-15 Identities = 44/175 (25%), Positives = 87/175 (49%), Gaps = 8/175 (4%) Query: 64 LHVTVTAILVPVMAVFFGIFETQAALNNFANSIIFLFLGGFALAAAMHHQGLDKVIADKV 123 L + + + + V + + A + IFLF G ALA A+ G ++A + Sbjct: 244 LPIAIIGSIGALSLVMTRVITEKQAYQAIDSQTIFLFGGTLALAKALETTGAGAIMARSI 303 Query: 124 LAMAQGKMSVAVFM--LFGVTALLSMWISNTATAAMMLPLVLGVLSKVDADKQRSTYVFV 181 + + + S + + + ++ +L+ ++SNTATAA+++P+ L + + AD + V Sbjct: 304 IDLLGHQASPFLLLSAVLIISCILTNFMSNTATAALLMPIGLSIAHSMGADPRA-----V 358 Query: 182 LLGVAYSASIGGIATLVGSPPNAIAAAEVGLSFTDWMKFGLPTAMMMLPMAIAIL 236 L+ + S AT VG+P N + + G F D++K GLP ++ + ++ +L Sbjct: 359 LMAIVIGCSCA-YATPVGTPANMMIFSAGGYKFVDYVKVGLPLILISVIVSFILL 412 Lambda K H 0.329 0.139 0.417 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: 463 Number of extensions: 26 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 462 Length of database: 419 Length adjustment: 32 Effective length of query: 430 Effective length of database: 387 Effective search space: 166410 Effective search space used: 166410 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