Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate WP_045583805.1 AL072_RS25785 TRAP transporter large permease
Query= reanno::SB2B:6938090 (466 letters) >NCBI__GCF_001305595.1:WP_045583805.1 Length = 428 Score = 233 bits (593), Expect = 1e-65 Identities = 156/455 (34%), Positives = 241/455 (52%), Gaps = 39/455 (8%) Query: 3 IATLFLTLFLCMLLGMPIAIALGFSSMLTILLFSNDSLASVALKLYEATSEHYTLLAIPF 62 IA + ++ LG+P+ + +G +L + + ++ +LA++ + L+E + + LLA+P Sbjct: 6 IALISVSAVGLFALGVPLVLIIGHW-VLWVSIVTDFTLANLGVTLFEGIN-FFGLLALPL 63 Query: 63 FILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSI 122 FIL+ ++ G+A+R+ DFA ++ +RGGL MA++ AC +FAA+SGS+ AT A IGSI Sbjct: 64 FILTGDIINAAGIAKRLTDFAYSTLSWVRGGLGMAAIGACGMFAAISGSNAATTATIGSI 123 Query: 123 VIVGMVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLLM 182 + M Y F+A + + G +GI+IPPSIV ++Y +S +FMAGLIPG LM Sbjct: 124 MYREMRDGKYGANFSAATLASGGVVGIIIPPSIVFVIYGFLMNLSIGDLFMAGLIPGALM 183 Query: 183 GVLLMVAIYIVARIKNLPSRPFPGVKALSL-SSAKAMGGLALIFIVLGSIYGGVASPTEA 241 +L M A+ IV +N P +SL S +A G I IVL IY G+ SPTEA Sbjct: 184 -ILAMQAVCIVVSWRNSWGEVVPFKAGVSLRSGLRAYLGFMAIGIVLFGIYSGIFSPTEA 242 Query: 242 AAVACVYAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHVGLGLIKTPTDKEIRN 301 AA+ V+ ++ E+ WR + Sbjct: 243 AAMTVVFGFVAGTL------VTGEIRWR----------------------------SLPT 268 Query: 302 VVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWGFLIIVNLLLLAA 361 V+ +++ ML+ ++A +++ +L+ IA + G G + L I + +L A Sbjct: 269 VLLRSGQIAGMLVPLVALSIVMQQLLSIIGTQAFIANLLSGIG-GYYATLGISMITVLIA 327 Query: 362 GNFMEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGITG 421 G F+E I +I+APIL PIA GIDPI ++ V+ IG +TPP GLNLFV + ITG Sbjct: 328 GCFLESVPITIILAPILAPIAHAAGIDPIQFAMVFVIGAAIGFITPPFGLNLFVASSITG 387 Query: 422 RSIGWVIHACLPWLLLLLGFLVLITYVPQISLFLP 456 ++ +P+L LL L+ VP S FLP Sbjct: 388 IPYLRIVPYVMPYLFALLIAWGLVALVPAFSTFLP 422 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: 598 Number of extensions: 36 Number of successful extensions: 4 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: 428 Length adjustment: 33 Effective length of query: 433 Effective length of database: 395 Effective search space: 171035 Effective search space used: 171035 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 24 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