Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate PfGW456L13_1086 L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1)
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1086 Length = 392 Score = 248 bits (632), Expect = 2e-70 Identities = 134/268 (50%), Positives = 186/268 (69%), Gaps = 4/268 (1%) Query: 6 ISKIEVKNVFKIFGNRSKEALELIRQNKTKDQVLAETGCVVGVNDLSLSIGTGEIFVIMG 65 +S I NV IF +EAL+L+ Q T++++L +TG +VGV SL I GEI V+MG Sbjct: 1 MSIIRFDNVDVIFSKDPREALKLLDQGMTRNEILKKTGQIVGVEKASLDIEKGEICVLMG 60 Query: 66 LSGSGKSTLVRHFNRLIDPTSGAILVDGE----DILQLDMDALREFRRHKISMVFQSFGL 121 LSGSGKS+L+R N L + G + V+ E DI L+ R +I+MVFQ F L Sbjct: 61 LSGSGKSSLLRCINGLNTVSRGKLFVEHEGKQIDIASCTPAELKMMRTKRIAMVFQKFAL 120 Query: 122 LPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLAR 181 +P +V +N+++GL+++G ++ + + VGL + NK P++LSGGM+QRVGLAR Sbjct: 121 MPWLTVRENISFGLEMQGRPEKERRKLVDDKLELVGLTQWRNKKPNELSGGMQQRVGLAR 180 Query: 182 ALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIAI 241 ALA D DI+LMDE FSALDPLIR +QD+LLELQ+ L KTIVF++HDLDEA+++G+RIAI Sbjct: 181 ALAMDADILLMDEPFSALDPLIRQGLQDELLELQRKLSKTIVFVSHDLDEALKLGSRIAI 240 Query: 242 LKDGKLIQVGTPREILHSPADEYVDRFV 269 +KDG++IQ P EI+ +PAD+YV FV Sbjct: 241 MKDGRIIQYSVPEEIVLNPADDYVRTFV 268 Lambda K H 0.321 0.138 0.387 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: 326 Number of extensions: 14 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: 276 Length of database: 392 Length adjustment: 28 Effective length of query: 248 Effective length of database: 364 Effective search space: 90272 Effective search space used: 90272 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 (21.9 bits) S2: 49 (23.5 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