Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Pf1N1B4_1346 Urea ABC transporter, ATPase protein UrtD
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1346 Length = 289 Score = 137 bits (346), Expect = 2e-37 Identities = 91/251 (36%), Positives = 139/251 (55%), Gaps = 13/251 (5%) Query: 9 VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68 +L + IS F G +AL+D+ + I G++ +IGPNGAGKTT +VITG P G Sbjct: 48 ILTLEDISVSFDGFKALNDLNLYIGVGELRCIIGPNGAGKTTLMDVITGKTRPSHGK-AW 106 Query: 69 AGKPYEPTAVHEV--AKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAV-FRTK 125 G+ + T + EV A+AGI R FQ +F ++ EN+ + + +T ++ ++ R Sbjct: 107 FGETLDLTQMSEVQIAQAGIGRKFQKPTVFEALSVFENLELAQ--KTDKSVWASLRARLS 164 Query: 126 GFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPA 185 G + + R E+L+ + + + A LS+G ++ LEI L DPQL+ LDEP Sbjct: 165 GEQKD------RISEVLETIRLTASVNRPAGMLSHGQKQFLEIGMLLMQDPQLLLLDEPV 218 Query: 186 AGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQ 245 AGM E EL + +++++EHD+ V + D VTVL G +AEG+ +VQ Sbjct: 219 AGMTDAETEFTAELFKSLAG-KHSLMVVEHDMGFVGSIADHVTVLHQGSVLAEGSLEQVQ 277 Query: 246 KNEKVIEAYLG 256 NE+VIE YLG Sbjct: 278 DNERVIEVYLG 288 Lambda K H 0.319 0.137 0.384 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: 197 Number of extensions: 11 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: 260 Length of database: 289 Length adjustment: 25 Effective length of query: 235 Effective length of database: 264 Effective search space: 62040 Effective search space used: 62040 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 (21.7 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