Align KguT (characterized, see rationale)
to candidate Pf1N1B4_5000 D-glycerate transporter (predicted)
Query= uniprot:A0A167V864 (425 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5000 Length = 436 Score = 201 bits (511), Expect = 4e-56 Identities = 132/414 (31%), Positives = 202/414 (48%), Gaps = 22/414 (5%) Query: 14 IMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAIYA 73 ++P +FI Y YLDR N GFA M D L + + L +FF+GY VP + Sbjct: 26 LIPFIFICYLFNYLDRVNVGFAKLQ-MLDALKFSETVYGLGAGIFFIGYVLCGVPSNLAL 84 Query: 74 EKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWFTR 133 K ++ I + +I WG L+T V + + +R G EA P +++YL WF Sbjct: 85 TKFGPRRWIALMMITWGTLSTCLLFVTTPTEFYTLRLFTGAAEAGFFPGVVLYLSQWFPT 144 Query: 134 AERSRANTFLILGNPVTILWMSVVSGYLVKHF--------DWRWMFIIEGLPAVLWAFIW 185 R R + PV+ L S SG+++ HF W+WMF+++G+P V+ + Sbjct: 145 FRRGRIMALFMSAIPVSGLLGSPFSGWILNHFGAGQAGLAGWQWMFLLQGIPTVILGALA 204 Query: 186 WRLVDDRPEQASWLKAQEKTALREALAAEQQGIKP---VKNYREAFRSPKVIILSLQYFC 242 + L+ D A WL E++ L EA A+ KP + F++P + L YFC Sbjct: 205 YFLLSDSYANAKWLTPYERSVL-EADHAQDLASKPKTATDSLLAVFKNPAIWAFGLIYFC 263 Query: 243 WSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVW 302 GVY WLPSI+K D + GWLSA+PYL A + ML V ++D ++R+ + Sbjct: 264 IQSGVYAINFWLPSIIKNLGFSDNLVIGWLSAIPYLLAAVFMLMVGRSADLRKERRWHLV 323 Query: 303 PPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYG-PFFAIVP-ELLPSNVAGGA 360 P+L+ A+ + + +L + A M A G P F VP +L + A G Sbjct: 324 VPMLMGAVGLLIAVNFAANP---AIAILGLTIATMGALTGLPMFWPVPTAMLSAGAAAGG 380 Query: 361 MALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGAL----LVAVALTAVL 410 +ALINSMG + F +LVG++ TG A+ + G + L+A+ +T L Sbjct: 381 LALINSMGQMAGFLSPYLVGWVKDSTGSTDAALYLLAGVIVCGSLLALRMTRTL 434 Lambda K H 0.328 0.140 0.457 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: 594 Number of extensions: 41 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 425 Length of database: 436 Length adjustment: 32 Effective length of query: 393 Effective length of database: 404 Effective search space: 158772 Effective search space used: 158772 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: 51 (24.3 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