Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_086510784.1 BZY95_RS15425 ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_002151265.1:WP_086510784.1 Length = 373 Score = 367 bits (942), Expect = e-106 Identities = 203/374 (54%), Positives = 254/374 (67%), Gaps = 11/374 (2%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA LE+ NV K +G LK++ L ID GEFLILVGPSGCGKSTLMN IAGLE ++ G Sbjct: 1 MAALEINNVCKDFGS--EQVLKDVSLAIDSGEFLILVGPSGCGKSTLMNAIAGLEPVTSG 58 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 I + ++ +P +RDIAMVFQSYALYP+M+VR NI+FGL++RK+P AE + V RV+ Sbjct: 59 EIRIAGESVTWQTPAERDIAMVFQSYALYPSMTVRQNISFGLEMRKVPKAEREAAVERVA 118 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 LLQI HLL RKP QLSGGQ+QRVAMGRALAR PK+YLFDEPLSNLDAKLRV+MRTE+K Sbjct: 119 DLLQIGHLLERKPSQLSGGQRQRVAMGRALAREPKVYLFDEPLSNLDAKLRVDMRTEIKK 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +HQRL TT VYVTHDQIEAMTL D +AVM+DG I Q G+P ++YN+P +LFVA F+GSP Sbjct: 179 LHQRLGTTIVYVTHDQIEAMTLADCIAVMRDGRILQLGSPDEVYNDPVDLFVAGFMGSPS 238 Query: 241 MNFIPLRLQRKDGRL-LALLDSGQARCELPLGM--QDAGLEDR---EVILGIRPEQIILA 294 MNFI L G L + G+ ELP + L ++ VILG+RPE Sbjct: 239 MNFISATLVGGSGAYRLRVETPGEETLELPWPQERETPALGEKVGERVILGLRPEHFTED 298 Query: 295 N---GEANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDP 351 + GE + + V EPTG D L+ + L D + R+ P GE LTL+ D Sbjct: 299 DARLGEYAEGVALTPRITVVEPTGADILLQLKLGDGEATARVGPKCRVKAGERLTLRIDM 358 Query: 352 AKVLLFDAKTGERL 365 + ++FD +T +RL Sbjct: 359 GRAVMFDRETEKRL 372 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: 472 Number of extensions: 22 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: 373 Length adjustment: 30 Effective length of query: 356 Effective length of database: 343 Effective search space: 122108 Effective search space used: 122108 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