Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_090440405.1 BLS63_RS04550 urea ABC transporter permease subunit UrtB
Query= TCDB::Q8DQI0 (292 letters) >NCBI__GCF_900100495.1:WP_090440405.1 Length = 523 Score = 119 bits (299), Expect = 1e-31 Identities = 85/290 (29%), Positives = 148/290 (51%), Gaps = 12/290 (4%) Query: 4 MLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQ----- 58 +L Q +GL LGS+ L ALG + +G++ +IN AHG++ M+GA+ Y + FQ Sbjct: 227 LLGQAFSGLSLGSILLLAALGLAITFGLLGVINMAHGEMLMLGAYATYMVQILFQRLAPE 286 Query: 59 ---MNFFVALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVG 115 + VAL VA TA +G+ +E R L + + L+ G+S +L + L G Sbjct: 287 ALALYPLVALPVAFFVTAAIGMALERTVIRHL-YGRPLETLLATWGISLMLIQMVRVLFG 345 Query: 116 ANT--RAFPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSV 173 A A P + L + L +++I+G +L +++L +++ KT++G +RAV+ Sbjct: 346 AQNVEVANPYWLSGGIAVLPNLVLPYNRIVIVGFALCVVLLTWLLLNKTRLGLNVRAVTQ 405 Query: 174 DSDAAQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLG 233 + + A G+ R F LGS +AG GV ++ N + P +G + + SF+ VLG Sbjct: 406 NRNMAACCGVPTGRVDMLAFGLGSGIAGLGGVALSQIGN-VGPDLGQSYIIDSFLVVVLG 464 Query: 234 GIGIIPGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGI 283 G+G + G+ L F +GL + ++ +++L + RP G+ Sbjct: 465 GVGQLAGSVLAAFGLGLANKILEPQIGAVLGKILILALIILFIQKRPQGL 514 Lambda K H 0.330 0.146 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: 296 Number of extensions: 13 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: 292 Length of database: 523 Length adjustment: 30 Effective length of query: 262 Effective length of database: 493 Effective search space: 129166 Effective search space used: 129166 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: 50 (23.9 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