Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate GFF3833 PGA1_262p02370 putative histidine transport system permease protein HisQ
Query= reanno::pseudo3_N2E3:AO353_03050 (229 letters) >FitnessBrowser__Phaeo:GFF3833 Length = 250 Score = 178 bits (451), Expect = 1e-49 Identities = 93/215 (43%), Positives = 137/215 (63%), Gaps = 1/215 (0%) Query: 4 GYGAVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIPDLV 63 G+G +L G +LQ+AL + + +++GL G +L L L +Y+TVIR +P+LV Sbjct: 23 GWGGNLLRGLANSLQIALGAFGMGLIIGLFGAYGKLYGGPILRDLLAIYTTVIRAVPELV 82 Query: 64 LILLIFYGGQDLLNRVAPLLGYDDYIDLNPLVAGIGTLGFIFGAYLSETFRGAFMAIPKG 123 LIL+++Y G DL+N+VA LGY ++++ +VAGI LG + GAY +E RGA A+P G Sbjct: 83 LILILYYVGTDLINKVAGSLGYGR-VEISGIVAGIWVLGIVQGAYATEVLRGAIKAVPPG 141 Query: 124 QAEAGAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQ 183 Q EA +YGM F RV +P M+ A PG N WL+ TK TAL+++VG ++ + +Q Sbjct: 142 QIEAARSYGMPPFMTMRRVTIPAMMSFATPGLANLWLIATKDTALLAIVGFAELTLETRQ 201 Query: 184 AADATREPFTFFLAVAAMYLVITSVSLLALRHLEK 218 AA +TR FTFFLA A+YL+IT S + +E+ Sbjct: 202 AASSTRAYFTFFLAAGALYLMITLCSSVIFGWIER 236 Lambda K H 0.329 0.144 0.421 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: 227 Number of extensions: 15 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: 229 Length of database: 250 Length adjustment: 23 Effective length of query: 206 Effective length of database: 227 Effective search space: 46762 Effective search space used: 46762 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 (21.8 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