Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate WP_092346318.1 BLU87_RS07515 C4-dicarboxylate ABC transporter permease
Query= reanno::SB2B:6938090 (466 letters) >NCBI__GCF_900107645.1:WP_092346318.1 Length = 466 Score = 677 bits (1746), Expect = 0.0 Identities = 345/466 (74%), Positives = 400/466 (85%), Gaps = 1/466 (0%) Query: 1 MTIATLFLTLFLCMLLGMPIAIALGFSSMLTILLFSNDSLASVALKLYEATSEHYTLLAI 60 MT LFL L LC+L GMPIA ALG SS+ TIL+FSNDSLAS+ALKL+ + SEHYTLLAI Sbjct: 1 MTTGALFLILLLCLLTGMPIAFALGLSSITTILIFSNDSLASIALKLFASQSEHYTLLAI 60 Query: 61 PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120 PFFILSS FLSTGGVA RII+FA+D VG IRGGLAMASVMACM+FAAVSGSSPATVAAIG Sbjct: 61 PFFILSSTFLSTGGVANRIINFAIDCVGWIRGGLAMASVMACMIFAAVSGSSPATVAAIG 120 Query: 121 SIVIVGMVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGL 180 SIVIVGMV+AGYP+ AAGVIT +GTLGILIPPSIVMLVYAAATE SAAR+FMAGL+PGL Sbjct: 121 SIVIVGMVKAGYPESLAAGVITNAGTLGILIPPSIVMLVYAAATEESAARLFMAGLVPGL 180 Query: 181 LMGVLLMVAIYIVARIKNLPSRPFPGVKALSLSSAKAMGGLALIFIVLGSIYGGVASPTE 240 LMG++LM+ IYIVAR+K LP++P+ G K L+ SS A GL +I IVLGSIYGG+ SPTE Sbjct: 181 LMGIMLMIIIYIVARVKGLPAQPWVGFKNLARSSMSAGWGLMMIVIVLGSIYGGICSPTE 240 Query: 241 AAAVACVYAYLVAVFGYRDIGPLKEVPWRK-EGEAILAAIVRNLLHVGLGLIKTPTDKEI 299 AAA++ VYA+ +A+F YRD+GPLK +PW++ ++I I RNL + L K+ DK++ Sbjct: 241 AAAISAVYAFFIAMFIYRDMGPLKGIPWKENHNDSIAKMIFRNLQLSVVALPKSIFDKDL 300 Query: 300 RNVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWGFLIIVNLLLL 359 V RD +KVSIMLLFII NAMLFAHVLTTERIPH IAE IVGWGLP WGFL++VN+LLL Sbjct: 301 HKVFRDASKVSIMLLFIIGNAMLFAHVLTTERIPHHIAEIIVGWGLPAWGFLVVVNILLL 360 Query: 360 AAGNFMEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGI 419 AGNFMEPSAILLIMAPILFPIAV+LGIDPIHLGIIMVVNMEIGM+TPPVGLNLFVTAGI Sbjct: 361 MAGNFMEPSAILLIMAPILFPIAVKLGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTAGI 420 Query: 420 TGRSIGWVIHACLPWLLLLLGFLVLITYVPQISLFLPEYLDSLRGF 465 TG +I WV+ A LPWLL+LL FL++ITY+PQISL+LPEY+D L+G+ Sbjct: 421 TGHNITWVLKAALPWLLVLLTFLIMITYIPQISLWLPEYIDHLKGY 466 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: 760 Number of extensions: 31 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: 466 Length of database: 466 Length adjustment: 33 Effective length of query: 433 Effective length of database: 433 Effective search space: 187489 Effective search space used: 187489 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