Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate PfGW456L13_84 Urea ABC transporter, ATPase protein UrtD
Query= TCDB::P73650 (240 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_84 Length = 290 Score = 102 bits (254), Expect = 8e-27 Identities = 86/247 (34%), Positives = 127/247 (51%), Gaps = 21/247 (8%) Query: 4 LLVVKDV---FAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQG 60 +L ++D+ F G+ A L +N I GEL +IGPNGAGK+TL I G PS G Sbjct: 49 ILTLEDISVSFDGFRA----LNNLNLYIGVGELRCIIGPNGAGKTTLMDVITGKTRPSHG 104 Query: 61 EIIFKGE--NITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMG--------AFLHQG 110 + F GE ++T + QI + G+ Q VF +L+V ENL++ A L Sbjct: 105 KAWF-GETLDLTQMSEVQIAQAGIGRKFQKPTVFEALSVFENLELAQKTDKSVWASLRAR 163 Query: 111 PTQTLKDRIYTMFP--KLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALS 168 + KDRI + +L N+ AG LS G++Q L +G LM DP LLLLDEP A ++ Sbjct: 164 LSGEQKDRIAQVLDTIRLTSSVNRPAGLLSHGQKQFLEIGMLLMQDPQLLLLDEPVAGMT 223 Query: 169 PILVKDVFAQIKAINATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPL 228 + K++ A ++++VE + +AD VL G EGS + + ++ Sbjct: 224 DAETEFTAELFKSL-AGKHSLMVVEHDMGFVGSIADHVTVLHQGSVLAEGSLEQVQDNER 282 Query: 229 VGELYLG 235 V E+YLG Sbjct: 283 VIEVYLG 289 Lambda K H 0.320 0.139 0.393 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: 150 Number of extensions: 6 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: 240 Length of database: 290 Length adjustment: 25 Effective length of query: 215 Effective length of database: 265 Effective search space: 56975 Effective search space used: 56975 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: 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