Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_086509603.1 BZY95_RS08775 urea ABC transporter permease subunit UrtB
Query= TCDB::P74318 (286 letters) >NCBI__GCF_002151265.1:WP_086509603.1 Length = 524 Score = 130 bits (328), Expect = 5e-35 Identities = 86/295 (29%), Positives = 150/295 (50%), Gaps = 27/295 (9%) Query: 4 SQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTW-----WANTSGIN 58 ++ ++ G+++GS++ L A+GL +T+G++ + N AHG+ + L AY TW G+ Sbjct: 232 AETLYFGLSLGSVLVLAAIGLAITFGVMGVINMAHGELIMLGAYTTWAMQQLLPGQPGLA 291 Query: 59 LWLSMALGCV-----GTIIAMFIGEWLLWKPMRARRATATTLIIIS----IGLALFLRNG 109 L L++ G + G I + ++L +P+ AT +I+ G++ R Sbjct: 292 LILAIPAGFLVAALAGIAIERGVIQFLKGRPLETLLATFGISLILQQLVRTGISPLNRTV 351 Query: 110 ILLIWGGNNQNYRVPIVPAQDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRA 169 I W + + D + + R+ V+ A+ VL LI++RT++G +RA Sbjct: 352 ITPEWMSGS-------IAVNDALSLTLN--RMYVLGFALVVFAVLMLIMRRTRLGLEVRA 402 Query: 170 VADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASVI 229 V N +A+ GI V + T+ + + + L G +T + PN+G I+ F V+ Sbjct: 403 VTQNRAMARSMGIRATRVDIMTFALGSGVAGLAGVALSQLTNVGPNLGQNYIIDSFMVVV 462 Query: 230 LGGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFI--RPQGLF 282 GG+GN +G + G+ +GV +V PW G M ++L+ IILFI RP+GLF Sbjct: 463 FGGVGNLWGTLVAGLSLGVINQVLEPWAGA--VMAKIIVLVFIILFIQKRPRGLF 515 Lambda K H 0.329 0.143 0.450 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: 318 Number of extensions: 15 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: 286 Length of database: 524 Length adjustment: 30 Effective length of query: 256 Effective length of database: 494 Effective search space: 126464 Effective search space used: 126464 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