Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_007700807.1 AFK65_RS15775 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_001277175.1:WP_007700807.1 Length = 375 Score = 307 bits (787), Expect = 3e-88 Identities = 172/379 (45%), Positives = 243/379 (64%), Gaps = 16/379 (4%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA + + K Y G + I+LKI DGEF+++VGPSGC KST + +AGLETISGG Sbjct: 1 MAEVIFNKLEKVYSNGFK-AVHGIDLKIADGEFMVIVGPSGCAKSTTLRMLAGLETISGG 59 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 + + + ++ ++PK+R IAMVFQ+YALYP M+VR+N+AFGLK+ K+P +I+ +V + Sbjct: 60 EVRIGEKLVNNLAPKERGIAMVFQNYALYPHMTVRENLAFGLKLSKLPKDQINRQVDEAA 119 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 K+L++E LL R P QLSGGQ QRVA+GRA+ ++P ++LFDEPLSNLDAKLR MR + Sbjct: 120 KILELEELLDRLPRQLSGGQAQRVAVGRAIVKKPDVFLFDEPLSNLDAKLRASMRIRISD 179 Query: 181 MHQRLK-----TTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASF 235 +H++LK TTVYVTHDQ EAMT+GD++ VMK G I Q TP ++Y+ P N+FVA F Sbjct: 180 LHKQLKKSGKPATTVYVTHDQTEAMTMGDRICVMKLGHIMQVDTPDNLYHYPKNMFVAGF 239 Query: 236 IGSPPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQD--AGLEDREVILGIRPEQIIL 293 IG+P MN P +L + G+LL + G R L Q+ A ++V GIRPE I + Sbjct: 240 IGAPEMNIKPGKLVEEAGQLLICI--GDNRLALTPRQQEKVAAYAGQQVFFGIRPEYISI 297 Query: 294 ANGEANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVA-PAVGETL----TLQ 348 ++ P E+ E G + V++ + D ++ CR+ D A P + + L + Sbjct: 298 SD-TPYAEPCGAGELVRVENMGHEFFVYLKVADFEMTCRIPSDEAKPMIDKGLHRKVYFK 356 Query: 349 FDPAKVLLFDAKTGERLGV 367 FD K LFDAKT + L + Sbjct: 357 FDMNKCHLFDAKTEQNLSL 375 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: 422 Number of extensions: 17 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: 375 Length adjustment: 30 Effective length of query: 356 Effective length of database: 345 Effective search space: 122820 Effective search space used: 122820 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 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