Align Galactofuranose-binding protein YtfQ (characterized)
to candidate H281DRAFT_02173 H281DRAFT_02173 monosaccharide ABC transporter substrate-binding protein, CUT2 family
Query= SwissProt::P39325 (318 letters) >FitnessBrowser__Burk376:H281DRAFT_02173 Length = 343 Score = 199 bits (505), Expect = 1e-55 Identities = 118/287 (41%), Positives = 159/287 (55%), Gaps = 7/287 (2%) Query: 7 IVSAVSAAMSSMALAAPLTVGFSQVGSESGWRAAETNVAKSEAEKRGITLKIADGQQKQE 66 I + A+ + PL VGF+Q S + WR AET K A K G L + D Sbjct: 38 IAAHAEDALPKLPGKTPLKVGFAQTESNNPWRLAETRSFKEVAAKCGWQLVMTDANGSNS 97 Query: 67 NQIKAVRSFVAQGVDAIFIAPVVATGWEPVLKEAKDAEIPVFLLDRSIDVKDKSL---YM 123 Q+ ++S +AQ VD + P PV+ +AK A IPV L+DR++D Y+ Sbjct: 98 KQVSDIQSMIAQHVDLLVFPPREEKPLAPVVLQAKKAGIPVILVDRNVDQSVAVAGRDYI 157 Query: 124 TTVTADNILEGKLIGDWLVKEVNGKPCNVVELQGTVGASVAIDRKKGFAEAIKNAPNIKI 183 T + +D I +G DWLVK GK ++EL+GT GAS A DRKKGF E I P + I Sbjct: 158 TFIGSDFIDQGHRAADWLVKATGGK-AKIIELEGTTGASAANDRKKGFDEIIAKNPGMTI 216 Query: 184 IRSQSGDFTRSKGKEVMESFIKAENNGKNICMVYAHNDDMVIGAIQAIKEAGLKPGKDIL 243 I SQSGDF R KG++VME+ ++A ++ VYAHND+M +GAI AIK AG +PGKDI Sbjct: 217 IASQSGDFARDKGRQVMETLLQAH---PDVTAVYAHNDEMALGAIAAIKAAGKQPGKDIQ 273 Query: 244 TGSIDGVPDIYKAMMDGEANASVELTPNMAGPAFDALEKYKKDGTMP 290 +IDG A+ GE ASV+ +P A D ++Y K +P Sbjct: 274 IVTIDGTKGGLDAIAAGELGASVQSSPFFGPLACDVAQRYAKGEKIP 320 Lambda K H 0.313 0.130 0.363 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: 250 Number of extensions: 10 Number of successful extensions: 4 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: 318 Length of database: 343 Length adjustment: 28 Effective length of query: 290 Effective length of database: 315 Effective search space: 91350 Effective search space used: 91350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 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