Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate SMa0250 SMa0250 dedA-like protein
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__Smeli:SMa0250 Length = 425 Score = 262 bits (670), Expect = 1e-74 Identities = 146/451 (32%), Positives = 249/451 (55%), Gaps = 35/451 (7%) Query: 1 MTIATLFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAI 60 MT+ +SL M +G+P+A +L F ++ + + +A + ++ +TLLAI Sbjct: 1 MTLVVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAG-ADTFTLLAI 59 Query: 61 PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120 PFFIL+ ++ GG++RRIIDFA+ VGHIRGGL + ++MA ++ A++SGS+ A AA+ Sbjct: 60 PFFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALA 119 Query: 121 SIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGL 180 +I+I M +AGY +AG+I G + +IPPS+ +V+ A VS ++FMAG++PGL Sbjct: 120 AILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGL 179 Query: 181 MMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASPTE 240 +MG+ L+ +V R + P + ++ +A+ L + VI+LG I G+ +PTE Sbjct: 180 IMGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTE 239 Query: 241 AAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKEIR 300 AA VA VYA F+ + YR++ P +++ Sbjct: 240 AAVVAAVYALFVGMVIYRELKP----------------------------------RDLP 265 Query: 301 HVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLLLA 360 V+ AK + +++F++ A++ + ++T IP I I + + ++ L++L Sbjct: 266 GVILQAAKTTAVIMFLVCAALVSSWLITAANIPSEITGFISPLIDRPTLLMFVIMLVVLV 325 Query: 361 AGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGIT 420 G ++ + +LI+ P+L PI Q GIDP++ G++ ++N IG+LTPPVG+ L V +G+ Sbjct: 326 VGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVLFIMNTCIGLLTPPVGVVLNVVSGVG 385 Query: 421 GRSMGWVIHSCIPWLALLLFFLALITYIPQI 451 +G VI P+L + L L+ P I Sbjct: 386 RVPLGKVIVGVTPFLVAQILVLFLLVLFPDI 416 Lambda K H 0.330 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: 575 Number of extensions: 37 Number of successful extensions: 5 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: 465 Length of database: 425 Length adjustment: 32 Effective length of query: 433 Effective length of database: 393 Effective search space: 170169 Effective search space used: 170169 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