Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate WP_012385497.1 BIND_RS12840 MFS transporter
Query= reanno::Koxy:BWI76_RS23715 (445 letters) >NCBI__GCF_000019845.1:WP_012385497.1 Length = 437 Score = 301 bits (771), Expect = 3e-86 Identities = 163/428 (38%), Positives = 248/428 (57%), Gaps = 7/428 (1%) Query: 2 SAINEKAVNGTQLQRT-HKKIYRHLMPLLIVAYIISFIDRTNIGMAKATMSVDIGLSATA 60 S+ AV+ L++ +K+ ++P+L + Y+ +F+DRTNIG A M+ DIGLSA+ Sbjct: 9 SSFASLAVDDDALKKAAFRKVIWRMLPILTLGYVFNFLDRTNIGFAALQMNRDIGLSASQ 68 Query: 61 FGLGAGLFFLTYAVLEIPSNLFLTRIGARRWIARIMITWGIISCGMAFVTGPTSFYVMRL 120 FG GAG+ F+ Y E+PSN+ L R GAR WI+RI+I+WG++SC M+ V+GPTSFY+MR Sbjct: 69 FGWGAGILFIGYCGFEVPSNILLYRFGARLWISRILISWGLLSCAMSLVSGPTSFYLMRF 128 Query: 121 LLGAAEAGLYPGIIYYLTLWFGREERAKATGLFLLGVCLANIIGAPLGGLLLSLDGMSGW 180 LG AEAG +PG+ Y+L+ WF + RA+ FL+ + ++++IG PLGGLLL LDG G Sbjct: 129 ALGVAEAGFFPGVAYFLSAWFPAQYRARILSWFLVAIPVSSVIGGPLGGLLLELDGHLGL 188 Query: 181 HGWQWMFFIEGLPAIALAFVVWRRLPDKPADARWLDSHDVQAITAVLEKEAEETRHTPSR 240 GWQW+F IEG+PA+ + V+ ++L D+P DA WL + + I A +E E + +R Sbjct: 189 AGWQWLFIIEGIPAVIIGLVLLKQLADRPQDAAWLTPDEKRVIVASVESEKRD--RVVNR 246 Query: 241 FSLKTALTTRVFLLLVLIYFTHQFSVYGLSYFLPGIIGSWGQLTPLQIGLLTAIPWIAAA 300 L AL + ++Y YG+ +LP I+ L+ LQIG ++A+P++AA+ Sbjct: 247 LGL--ALRDIRVWMCTIVYLGFTVGSYGVQIWLPQIL-KQQNLSNLQIGWISALPYLAAS 303 Query: 301 AGGILLPRFARTEQRSRSMLMAGYLVMATGMAIG-AIAGHGVALLGFSLAAFMFFAMQSI 359 G I+ FA R L + G + A ++LLG + A ++I Sbjct: 304 VGMIIWAGFADRSGRKIINLSTCCFLAVVGFVLAIATRRFDLSLLGLTAALVGVTGARAI 363 Query: 360 IFNWLPSIMSGHMLAGSFGLLNCLGLCGGFLGPFILGAFEDRTGAATSGLWFAVALLIVG 419 ++ ++G AG +N +G GGF GP I+G +D TG +GL L V Sbjct: 364 FWSIPTRFLTGIAAAGGIAFINTIGTTGGFFGPTIVGWLKDTTGTFEAGLLAMAGFLAVS 423 Query: 420 ALASLLIK 427 + +LL+K Sbjct: 424 TVFALLLK 431 Lambda K H 0.328 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: 498 Number of extensions: 20 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: 445 Length of database: 437 Length adjustment: 32 Effective length of query: 413 Effective length of database: 405 Effective search space: 167265 Effective search space used: 167265 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