Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate WP_041936920.1 RL_RS31840 sugar ABC transporter ATP-binding protein
Query= TCDB::Q7BSH4 (512 letters) >NCBI__GCF_000009265.1:WP_041936920.1 Length = 511 Score = 922 bits (2382), Expect = 0.0 Identities = 480/512 (93%), Positives = 494/512 (96%), Gaps = 1/512 (0%) Query: 1 MNAAFQQPVTDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKS 60 MNAAFQQ TDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKS Sbjct: 1 MNAAFQQTATDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKS 60 Query: 61 TLVKILTGIYRPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGH 120 TLVKILTGIYRPNEGEILVDG+P TFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGH Sbjct: 61 TLVKILTGIYRPNEGEILVDGQPVTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGH 120 Query: 121 APRTRFRTIDWQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVI 180 APRTR RTIDWQ MNSR+KALLTALESNIDPTIRLKD SIAQRHLVAIARALSIEARIVI Sbjct: 121 APRTRLRTIDWQAMNSRAKALLTALESNIDPTIRLKDFSIAQRHLVAIARALSIEARIVI 180 Query: 181 MDEPTAALSRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRG 240 MDEPTAALSRKEIDDLFRIVRGLKE+GKAILFISHKFDE+YEIADDFVVF R R +G Sbjct: 181 MDEPTAALSRKEIDDLFRIVRGLKEKGKAILFISHKFDEVYEIADDFVVF-RDGRAVGQG 239 Query: 241 VSRKTPQDEIVRMMVGRDVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILG 300 ++TPQDEIVRMMVGRDVEN FPK+DVA GGPVLEIRNYSHRTEFRDISFTLR+GEILG Sbjct: 240 RLKETPQDEIVRMMVGRDVENAFPKVDVAFGGPVLEIRNYSHRTEFRDISFTLRQGEILG 299 Query: 301 VYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLA 360 +YGLIGAGRSELSQSLFGIT+PLSGKM+LEG+EITIHSPQDAIRAGIVYVPEERGRHGLA Sbjct: 300 IYGLIGAGRSELSQSLFGITRPLSGKMMLEGREITIHSPQDAIRAGIVYVPEERGRHGLA 359 Query: 361 LPMPIFQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQK 420 LPMPIFQNMTLPSL RTSRRGFLRAA EFALARKYAERLDLRAAALSVPVGTLSGGNQQK Sbjct: 360 LPMPIFQNMTLPSLTRTSRRGFLRAAEEFALARKYAERLDLRAAALSVPVGTLSGGNQQK 419 Query: 421 VVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSD 480 VVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSD Sbjct: 420 VVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSD 479 Query: 481 RVLVMKEGLSAGIFERAELSPEALVRAATGNA 512 RVLVMKEGL+AGIFERAELSPEALVRAATGNA Sbjct: 480 RVLVMKEGLAAGIFERAELSPEALVRAATGNA 511 Lambda K H 0.320 0.137 0.382 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: 939 Number of extensions: 23 Number of successful extensions: 6 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: 512 Length of database: 511 Length adjustment: 35 Effective length of query: 477 Effective length of database: 476 Effective search space: 227052 Effective search space used: 227052 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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