Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate Pf1N1B4_3433 Arginine/ornithine ABC transporter, permease protein AotM
Query= uniprot:B2TBJ8 (250 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3433 Length = 232 Score = 185 bits (470), Expect = 6e-52 Identities = 95/222 (42%), Positives = 142/222 (63%) Query: 1 MHFDFDFLFDTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYIL 60 M FD++ +++ + L + TTL L SL G L +L + MRVS + N A + Sbjct: 1 MIFDYNVIWEALPLYLGGLVTTLKLLALSLFFGLLAALPLGLMRVSKQPVVNMSAWLFTY 60 Query: 61 VFRGSPLLIQMFLVYYGMGQFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGL 120 V RG+P+L+Q+FL+YYG+ QF +RESFLWP L CA L+ A+ T+ YTAEII G L Sbjct: 61 VIRGTPMLVQLFLIYYGLAQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSL 120 Query: 121 MAVPVGQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEV 180 A P G+IEA ++G+S + +R++ P ALR+ LP YS E ++++++T+LAS+VT+ ++ Sbjct: 121 RATPNGEIEAAKAMGMSRIKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDI 180 Query: 181 TGVAQQIIQQTYRTTEVFICAALIYLFLNFVIVRLLGMLETR 222 TG A+ + Q Y E +I A + YL L F++VRL M E R Sbjct: 181 TGAARTVNAQFYLPFEAYITAGVFYLCLTFILVRLFKMAEHR 222 Lambda K H 0.331 0.143 0.431 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: 166 Number of extensions: 3 Number of successful extensions: 1 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: 250 Length of database: 232 Length adjustment: 23 Effective length of query: 227 Effective length of database: 209 Effective search space: 47443 Effective search space used: 47443 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 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