Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate WP_049778410.1 RL_RS05180 MFS transporter
Query= reanno::WCS417:GFF1429 (438 letters) >NCBI__GCF_000009265.1:WP_049778410.1 Length = 445 Score = 310 bits (793), Expect = 8e-89 Identities = 167/413 (40%), Positives = 251/413 (60%), Gaps = 7/413 (1%) Query: 11 QALNKLMFVKLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYAL 70 + L K+ F +++P +++ Y ++FLDR NI A ++ DLG S+ +G+GAG+FF+ Y L Sbjct: 21 RVLRKITF-RIVPFIMLLYFIAFLDRVNIGFAALTMNQDLGFSSTVFGIGAGIFFVGYFL 79 Query: 71 SEIPSNLIMHKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVM 130 E+PSNLI++KVGAR WIAR+M+TWG++S MAFVQG TSFY LR LLG+AEAG FPG++ Sbjct: 80 FEVPSNLILNKVGARIWIARVMITWGIVSGLMAFVQGTTSFYALRFLLGVAEAGFFPGII 139 Query: 131 LYLTYWFNREQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPA 190 LYL++WF +RA T F+ + ++G P+ ALM M G LG GWQWMF++E PA Sbjct: 140 LYLSFWFPARRRAAVTAIFMAAAPLSTVLGSPISGALMEMHGFLGLAGWQWMFLIEAAPA 199 Query: 191 VAFAWVVWRKLPDRPSKAPWLSAEEARGIEQRIAQETEEGAGEGGHSLKNWLTP-QILLA 249 + VV L DRP KA WL+ EE + + + E + G + HS+ L +++ Sbjct: 200 IILGVVVLFYLTDRPEKAKWLTDEERSWLVKTMNAE-QAGKSKASHSILAGLADIRVIAL 258 Query: 250 IFVYFCHQITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPGR 309 VYF +YT+ + P II ++G LS + VG + ++P I A + +L R + G Sbjct: 259 ALVYFGTSAGLYTLGIWAPQIIKQFG-LSALQVGFINAIPGIFAVVAMILWARHSDKTGE 317 Query: 310 CRRLLVTGLLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQS--IIFLYPASRLKGVAL 367 +V L A GL A+ + V+++L L+ V + S ++ P L G A Sbjct: 318 RTWHVVGACLLAAAGLAFATGATSVYTVL-IALTLVNIGISSSKPPLWSMPTLFLSGPAA 376 Query: 368 AGGLGFVNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRL 420 A G+ +N+ G LGGFVGPS++G I+ +TG+ GL +A +L+++A+ L L Sbjct: 377 AAGIATINSIGNLGGFVGPSMIGWIKDTTGSFAGGLYFVAGLLMISAILTLVL 429 Lambda K H 0.327 0.141 0.438 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: 549 Number of extensions: 26 Number of successful extensions: 3 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: 438 Length of database: 445 Length adjustment: 32 Effective length of query: 406 Effective length of database: 413 Effective search space: 167678 Effective search space used: 167678 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 (21.7 bits) S2: 51 (24.3 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