Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate GFF3834 PGA1_262p02380 putative histidine transport system permease protein HisM
Query= reanno::pseudo1_N1B4:Pf1N1B4_3433 (232 letters) >FitnessBrowser__Phaeo:GFF3834 Length = 258 Score = 145 bits (367), Expect = 6e-40 Identities = 78/222 (35%), Positives = 125/222 (56%), Gaps = 8/222 (3%) Query: 9 WEALPLY----LGGLVTTLKLLALSLFFGLLAALPLGLMRVSKQPVVNMSAWLFTYVIRG 64 W+ +P Y L GL TT+ +L ++ G A+PLGL + ++ A +F VIRG Sbjct: 32 WDWIPTYAPLALEGLWTTIWILVVTSILGFALAVPLGLAQAVGPWYLSTPARIFCTVIRG 91 Query: 65 TPMLVQLFLIYYGLA----QFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSL 120 TP+L+Q++L+YYGL QF +R S LWP+L A A LA ++ + Y E++ G+ Sbjct: 92 TPLLLQIWLLYYGLGSLFPQFPWIRSSELWPYLRQAWPYAVLALTLSYAGYEGEVMRGAF 151 Query: 121 RATPNGEIEAAKAMGMSRIKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDI 180 G++EAAKA GM R+ M++RI LP A+R LP E I+ L+ T L + +T++DI Sbjct: 152 SGVAKGQLEAAKAYGMPRLTMFRRIWLPQAVRNVLPTLGGETILQLKATPLVATITVLDI 211 Query: 181 TGAARTVNAQFYLPFEAYITAGVFYLCLTFILVRLFKMAEHR 222 + V + ++ +E + + Y+ + ++ FK E R Sbjct: 212 YAVSSRVRSDTFIVYEPLLLLALVYMAIAGVITLAFKRFEDR 253 Lambda K H 0.330 0.140 0.427 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: 168 Number of extensions: 9 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: 232 Length of database: 258 Length adjustment: 24 Effective length of query: 208 Effective length of database: 234 Effective search space: 48672 Effective search space used: 48672 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 (21.9 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