Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__HerbieS:HSERO_RS16715 Length = 361 Score = 343 bits (881), Expect = 3e-99 Identities = 185/367 (50%), Positives = 248/367 (67%), Gaps = 11/367 (2%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA++++R V K +G ++ +++ I DGEF +LVGPSGCGKSTL+ +AGLE I+GG Sbjct: 1 MASVQIRAVKKQFGS--TQIIRGVDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 IL+ ++ + PKDRDIAMVFQ+YALYP M+VRDN+AF L + K A +DE V + + Sbjct: 59 EILIGGTVVNNVQPKDRDIAMVFQNYALYPHMTVRDNMAFSLTLAKKDKAFVDERVKKAA 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 +L + LL R P QLSGGQ+QRVAMGRA+ R P+++LFDEPLSNLDAKLRV+MRTE+K Sbjct: 119 DILGLNQLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKE 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +HQRLKTT++YVTHDQIEAMT+ D++ VM+DG+++Q G P D+Y+ PANLFVA FIGSP Sbjct: 179 LHQRLKTTSIYVTHDQIEAMTMADQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPA 238 Query: 241 MNFIPLRLQRK-DGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQI-ILANGEA 298 MNFIP L+R G + D R P G G + ++V G+RPE + I A G+ Sbjct: 239 MNFIPATLRRNATGAEVEFADG--TRVPAPYGAALQGNDGQKVTYGVRPEHLSIGAAGQG 296 Query: 299 NGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFD 358 I +V V EPTG DT VF DT + G+ + L D ++ LFD Sbjct: 297 -----IATKVIVVEPTGADTEVFSRFGDTSLTSIFRERHDFGAGDVIHLVPDHSRTHLFD 351 Query: 359 AKTGERL 365 A++G+ L Sbjct: 352 AESGKSL 358 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: 392 Number of extensions: 11 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: 361 Length adjustment: 30 Effective length of query: 356 Effective length of database: 331 Effective search space: 117836 Effective search space used: 117836 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: 50 (23.9 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