Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Miya:8499890 Length = 350 Score = 267 bits (682), Expect = 4e-76 Identities = 152/368 (41%), Positives = 225/368 (61%), Gaps = 23/368 (6%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 M+ ++L NV++ +G + ++ +++ G L+L+GPSGCGKST + IAGLE+++ G Sbjct: 1 MSAIQLLNVSRHWGD--VRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 I++ + D++ + P R +AMVFQSYAL+P ++VR+NI FGL +RK+P AE ++ + R Sbjct: 59 RIMIGERDVTHLPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRLTRAV 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 +L + LL RKPG+LSGGQQQRVA+GRAL + L DEPLSNLDAKLR EMR E++ Sbjct: 119 DILGLSALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMRREIRA 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 + Q L T VYVTHDQ EAM++ D++ +M+ G I Q TP ++Y+ PA F +FIG+PP Sbjct: 179 LQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNFIGTPP 238 Query: 241 MNFIPLRLQRKDGRL-LALLDSGQARCELPLGMQDAGLEDREVILGIRPEQI-ILANGEA 298 MN + RL G + +A SG + ++ + +LGIRPE I I+ G Sbjct: 239 MNLV--RLDDARGSVCVAGSRSGTV----------SVVDSADYVLGIRPEHIRIVPEG-- 284 Query: 299 NGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFD 358 RA V+ E G +++ + ++ + AVG + L + +FD Sbjct: 285 -----WRAVVESVEYLGSGSVLGCRVGGEELSVVVDGVPTIAVGAEIYLHCPDEHIHIFD 339 Query: 359 AKTGERLG 366 AKTGER G Sbjct: 340 AKTGERRG 347 Lambda K H 0.319 0.138 0.393 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: 334 Number of extensions: 15 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: 386 Length of database: 350 Length adjustment: 30 Effective length of query: 356 Effective length of database: 320 Effective search space: 113920 Effective search space used: 113920 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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