Align nucleoside permease nupG (characterized)
to candidate CA265_RS08855 CA265_RS08855 MFS transporter
Query= CharProtDB::CH_088596 (418 letters) >FitnessBrowser__Pedo557:CA265_RS08855 Length = 459 Score = 409 bits (1052), Expect = e-119 Identities = 206/451 (45%), Positives = 293/451 (64%), Gaps = 44/451 (9%) Query: 1 MNLKLQLKILSFLQFCLWGSWLTTLGSYMFVTLKFDGASIGAVYSSLGIAAVFMPALLGI 60 MN+K +L I+SF+QF +W +WL T+ +Y F T ++DGA G ++S++GIA++FMP + GI Sbjct: 1 MNVKFRLTIMSFMQFFVWAAWLITIANYWFGTKQWDGADFGIIFSTMGIASLFMPTITGI 60 Query: 61 VADKWLSAKWVYAICHTIGAITLFMAAQVTTPEAMFLVILINSFAYMPTLGLINTISYYR 120 +ADKW++A+ +YAI H + A T+F QV P F VIL+ YMPT+ L N+ISY Sbjct: 61 LADKWINAERLYAILHILYAATMFYLPQVEDPHTFFWVILVAMCFYMPTIALSNSISYTT 120 Query: 121 LQNAGMDIVTDFPPIRIWGTIGFIMAMWVVSLSGFELSHMQLYIGAALSAILVLFTLTLP 180 L+N D+V +FPPIR+WGT+GFI AMW+ +L+G + S Q YI + +L L++ TLP Sbjct: 121 LKNGNFDVVKNFPPIRVWGTVGFIAAMWLTNLTGNKASANQFYIAGVSALMLGLYSFTLP 180 Query: 181 HI-PVAKQQANQSWTTLLGLDAFALFKNKRMAIFFIFSMLLGAELQITNMFGNTFLHSFD 239 P+ +++ LGL++F LF + +MA+FFIFSM LGA LQ+TN +G+ FL F Sbjct: 181 ACKPLNLISEKKTFAQKLGLESFKLFADYKMALFFIFSMFLGAALQLTNAYGDVFLDEFK 240 Query: 240 KDPMFASSFIVQHASIIMSISQISETLFILTIPFFLSRYGIKNVMMISIVAWILRFALFA 299 P+FA SF++++++II+SISQISETLFIL IPFFL R+GIK V+ I++ AW+LRF LFA Sbjct: 241 LFPVFAESFVIRYSTIILSISQISETLFILAIPFFLKRFGIKWVIAIAMFAWVLRFGLFA 300 Query: 300 YGDPTPFGTVLLVLSMIVYGCAFDFFNISGSVFVEKEVSPAIRASAQGMFLMMTNGFGCI 359 +GDP+ +++ S IVYG AFDFFNISGS+FVE +P R+SAQG+F+MMTNGFG + Sbjct: 301 FGDPST-NLWMIITSCIVYGMAFDFFNISGSLFVETSTTPKTRSSAQGLFMMMTNGFGAV 359 Query: 360 LGGIVSGKVVEMY-----------------------------------TQNG-------I 377 G +VSG ++ Y +NG + Sbjct: 360 FGSLVSGWMINKYFTTYYSSIDSLSKYVKSEADNKHLLQFLKNKGISVLENGNLSRALDV 419 Query: 378 TDWQTVWLIFAGYSVVLAFAFMAMFKYKHVR 408 DW +WL F Y +V+A F+ +FK+KH R Sbjct: 420 KDWHNIWLSFTIYVLVIAIVFVVIFKHKHTR 450 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: 696 Number of extensions: 40 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 418 Length of database: 459 Length adjustment: 32 Effective length of query: 386 Effective length of database: 427 Effective search space: 164822 Effective search space used: 164822 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: 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