Align GlcU, component of Glucose, mannose, galactose porter (characterized)
to candidate BPHYT_RS05035 BPHYT_RS05035 sugar ABC transporter permease
Query= TCDB::Q97UY9 (287 letters) >FitnessBrowser__BFirm:BPHYT_RS05035 Length = 285 Score = 130 bits (328), Expect = 3e-35 Identities = 90/296 (30%), Positives = 148/296 (50%), Gaps = 21/296 (7%) Query: 1 MDKKMRPVIKASLHYLALAIVSVIWLIPVYAMLINGFKSNFEVLSTPVLVPPTKITFEAY 60 M KM I ++ Y AL + ++ +L P+Y ML FK ++ + +L PPT T + + Sbjct: 1 MQPKM--TISRAVIYAALFLFALYFLFPLYVMLSTSFKDIDQLRTGNLLTPPTHWTIDPW 58 Query: 61 VSVLLSLAKPL---------INSLIIVIPTSFISAFLGAMGAYFFYTLSYSFSRASSAIS 111 + + +NS+ +VIP IS+ +GA Y + F A Sbjct: 59 IKAWSGACTGVRCDGMQPFFMNSVRMVIPAVLISSIIGAFNGYVL--THWRFRGA----- 111 Query: 112 DVLFSLISLATFIPQEATLLPLTRLIVSMGLLDSYIGIIFALLIFYIPTGALLMSMFISV 171 D +F++I + FIP +A LLP+ R +GL ++ G++ +I+ I + F Sbjct: 112 DPIFTMILVGCFIPFQAILLPMARFEGFLGLSNTTTGLVVVHVIYGIAFTTMFFRNFYVS 171 Query: 172 IPRSLIEAAKMDGTGDLKIFMKIVFPLSMPGFISTLIFIIIQAWNNFFIPLVLVTTPGMK 231 IP L++AA++DG G IF KI+ P+S+P F+ LI+ Q WN+F +V M Sbjct: 172 IPAELVKAARIDGAGFFTIFTKILLPVSLPIFMVCLIWQFTQIWNDFLFGIVFSGVDSMP 231 Query: 232 LT-SIAVLSYSGAYGTLYNDTFAAGMVASIIPLAIFVFLGRYFIRGLMALGGGGKG 286 +T ++ L + YN A ++A++ L +++ GRYF+RGL A G KG Sbjct: 232 ITVALNNLVNTSTGVKEYNVDMAGAIIAALPTLLVYIIAGRYFVRGLTA--GAVKG 285 Lambda K H 0.330 0.144 0.417 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: 234 Number of extensions: 14 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: 287 Length of database: 285 Length adjustment: 26 Effective length of query: 261 Effective length of database: 259 Effective search space: 67599 Effective search space used: 67599 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: 47 (22.7 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