Align Fumarate (Na+-independent anion) transporter, SLC26dg of 499 aas and 14 TMSs (characterized)
to candidate CA265_RS24540 CA265_RS24540 sodium-independent anion transporter
Query= TCDB::Q1J2S8 (499 letters) >FitnessBrowser__Pedo557:CA265_RS24540 Length = 511 Score = 375 bits (963), Expect = e-108 Identities = 190/467 (40%), Positives = 300/467 (64%), Gaps = 12/467 (2%) Query: 20 NPRKDVLAGIVVALALIPEAIAFSIIAGVDPQVGLYASFIIALITAFLGGRPGMISAATG 79 N + ++LAG+ VA+ +IPE+++F+I+AG P GLYA+FI+ L+TA LGGRPG++S G Sbjct: 15 NYKTEILAGLTVAMTMIPESLSFAILAGFPPLTGLYAAFIMGLVTAILGGRPGLVSGGAG 74 Query: 80 AMALLMTGLVKDHGIQYLFAATVLTGVLQVVFGWAKLARYLKFVPRSVMVGFVNALAILI 139 A +++ L+K GI+Y+FAA L G++Q++ G KL ++++ VP+ VM GFVN LA++I Sbjct: 75 ATVIVLIALMKTQGIEYVFAAVALAGLIQIMVGLFKLGKFVRLVPQPVMFGFVNGLAVII 134 Query: 140 FMAQLPQFVGA-----NWQ-------MYAMVAAGLAIIYLLPLVFKAMPSALVAIVVLTV 187 FM+QL QF W M A+V +AI+ +LP + KA+P++LVAI+V+ + Sbjct: 135 FMSQLEQFKTLVDGRITWLSGTPLYVMLALVLLTVAIVIILPKITKAVPASLVAIIVVFL 194 Query: 188 VAVVTGADVKTVGDMGTLPTALPHFQFPQVPLTFETLAIIFPVALTLSLVGLLESLLTAQ 247 + + G D K V ++ ++ P F P+VPL + L IIFP +L ++ VGL E LLT Sbjct: 195 IVLCFGIDTKLVKNIASVNGGFPPFHIPKVPLNLDMLKIIFPYSLIMAGVGLTEGLLTLN 254 Query: 248 LIDERTDTTSDKNVESRGQGVANIVTGFFGGMAGCAMIGQSMINVTSGGRGRLSTFVAGA 307 L+DE T + ++N ES QG+ANI GFF GM GC MI Q+++N+++G R RLS +A Sbjct: 255 LVDEITASKGNRNRESIAQGIANIANGFFTGMGGCPMIAQTLVNLSAGARARLSGIIAAL 314 Query: 308 FLMVLILALQPLLVQIPMAALVAVMMVVAISTFDWGSLRTLTVFPKGETVVMLATVAVTV 367 ++++IL P++ ++PMAALV VMM+VAI TF+W S + + P + ++ + +TV Sbjct: 315 TILLIILVGAPVIDRVPMAALVGVMMMVAIGTFEWMSFKVINKMPAQDIIIGILVAVITV 374 Query: 368 FTHDLSLGVLIGVVLSALFFARKVSQLSQVTPVDEVDGTRTYRVRGQLFFVSTHDFLHQF 427 + H+L+L VLIGV+LSAL FA + S+ + + + G +TY + G LFF S +F F Sbjct: 375 WLHNLALAVLIGVILSALVFAWESSKRIRASKHTDASGVKTYEIFGPLFFGSIANFNELF 434 Query: 428 DFTHPARRVVIDLSDAHFWDGSAVGALDKVMLKFMRQGTSVELRGLN 474 D H + +VID + +D S + AL+K+ ++ ++L+ L+ Sbjct: 435 DVAHDPQHIVIDFKHSRVFDMSGIDALNKLTERYRSLDKKLQLKHLS 481 Lambda K H 0.328 0.140 0.407 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: 530 Number of extensions: 28 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: 499 Length of database: 511 Length adjustment: 34 Effective length of query: 465 Effective length of database: 477 Effective search space: 221805 Effective search space used: 221805 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 (21.7 bits) S2: 52 (24.6 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