Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate GFF3833 PGA1_262p02370 putative histidine transport system permease protein HisQ
Query= reanno::pseudo5_N2C3_1:AO356_00470 (220 letters) >FitnessBrowser__Phaeo:GFF3833 Length = 250 Score = 97.1 bits (240), Expect = 3e-25 Identities = 63/209 (30%), Positives = 106/209 (50%), Gaps = 11/209 (5%) Query: 18 LWAGFLTSVQCSLLAIVLGTLIGLVAGLVLTYGRTWMRAPFRFYVDLIRGTPVFVLVLAC 77 L G S+Q +L A +G +IGL YG +R Y +IR P VL+L Sbjct: 28 LLRGLANSLQIALGAFGMGLIIGLFGAYGKLYGGPILRDLLAIYTTVIRAVPELVLILIL 87 Query: 78 FYM--------APALGW---QIGAFQAGVLGLTLFCGSHVAEIVRGALQALPRGQMEASQ 126 +Y+ A +LG+ +I AG+ L + G++ E++RGA++A+P GQ+EA++ Sbjct: 88 YYVGTDLINKVAGSLGYGRVEISGIVAGIWVLGIVQGAYATEVLRGAIKAVPPGQIEAAR 147 Query: 127 AIGLTFYQSLGYVLLPQALRQILPTWVNSSTEIVKASTLLSVIGVAELLLSTQQIIARTF 186 + G+ + ++ V +P + P N K + LL+++G AEL L T+Q + T Sbjct: 148 SYGMPPFMTMRRVTIPAMMSFATPGLANLWLIATKDTALLAIVGFAELTLETRQAASSTR 207 Query: 187 MTLEFYLFAGFLFFIINYAIELLGRHIEK 215 F+L AG L+ +I ++ IE+ Sbjct: 208 AYFTFFLAAGALYLMITLCSSVIFGWIER 236 Lambda K H 0.330 0.142 0.443 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: 196 Number of extensions: 10 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: 220 Length of database: 250 Length adjustment: 23 Effective length of query: 197 Effective length of database: 227 Effective search space: 44719 Effective search space used: 44719 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