Align nucleoside permease nupG (characterized)
to candidate WP_057509062.1 ABB28_RS13210 MFS transporter
Query= CharProtDB::CH_088596 (418 letters) >NCBI__GCF_001431535.1:WP_057509062.1 Length = 405 Score = 242 bits (618), Expect = 1e-68 Identities = 128/406 (31%), Positives = 226/406 (55%), Gaps = 19/406 (4%) Query: 6 QLKILSFLQFCLWGSWLTTLGSYMFV-TLKFDGASIGAVYSSLGIAAVFMPALLGIVADK 64 +L + FLQF +WG+W TLG+Y+ L+ + + + S I A+ P L+G+VAD+ Sbjct: 7 RLGAMMFLQFFIWGAWFVTLGTYLVQGPLQASASQVATAFLSQSIGAIVAPFLVGLVADR 66 Query: 65 WLSAKWVYAICHTIGAITLFMAAQVTTPEAMFLVILINSFAYMPTLGLINTISYYRLQNA 124 + +A+ + A+ H GA+ ++MA+ + ++ +MPTL L N+++ +Q+ Sbjct: 67 YFAAQRILAVLHLAGAVLMWMASTASDFGTFSACVMGYMLLFMPTLALANSVAMRHMQSP 126 Query: 125 GMDIVTDFPPIRIWGTIGFIMAMWVVSLSGFELSH---MQLYIGAALSAILVLFTLTLPH 181 FP +R+ G++G+I+A ++ G+E +H + + A S L L+ TLPH Sbjct: 127 EKQ----FPLVRVAGSVGWIVAGVLIGWLGWEQAHRLELTFQMAAIASLALGLYAFTLPH 182 Query: 182 IPVAKQQANQSWTTLLGLDAFALFKNKRMAIFFIFSMLLGAELQITNMFGNTFLHSFDKD 241 P +Q + +LGLD+ L K++ +FF+ S+ + L F N +L+ Sbjct: 183 TPPLARQRDAGMGQILGLDSLRLLKSRSYLVFFLASIAICIPLAFYYNFTNPYLNDLG-- 240 Query: 242 PMFASSFIVQHASIIMSISQISETLFILTIPFFLSRYGIKNVMMISIVAWILRFALFAYG 301 V+ A+ + S+ Q+SE L +L +PF R G+K ++ + + AW++R+ +FA+G Sbjct: 241 --------VRGAAGLQSLGQVSEVLLMLAMPFLFVRLGVKTMLAVGMAAWVVRYVMFAFG 292 Query: 302 DPTPFGTVLLVLSMIVYGCAFDFFNISGSVFVEKEVSPAIRASAQGMFLMMTNGFGCILG 361 D G LLV+ ++++G +DFF ++G ++ + PA R+SAQG + T G G ++G Sbjct: 293 DAGG-GFSLLVIGIVLHGICYDFFFVTGQIYTDAHAGPAARSSAQGFITLATYGVGMLIG 351 Query: 362 GIVSGKVVEMYTQNGITDWQTVWLIFAGYSVVLAFAFMAMFKYKHV 407 +SG VVE YT DWQ +WL AG ++V+ AF+ +F+ + V Sbjct: 352 TFLSGAVVEHYTTAAGPDWQKIWLFPAGVALVVLIAFLLLFRDRPV 397 Lambda K H 0.331 0.141 0.436 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: 490 Number of extensions: 29 Number of successful extensions: 6 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: 418 Length of database: 405 Length adjustment: 31 Effective length of query: 387 Effective length of database: 374 Effective search space: 144738 Effective search space used: 144738 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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