Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__PV4:5208351 Length = 342 Score = 191 bits (484), Expect = 3e-53 Identities = 118/310 (38%), Positives = 185/310 (59%), Gaps = 18/310 (5%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 M+TL + V+ Y L+ ++L + GE L+GPSGCGK+TL+ IAGL+ IS G Sbjct: 1 MSTLTIEQVHSDYQG--QTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQG 58 Query: 61 AILVDDADISG----MSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEV 116 I ++ +SG + + R++ M+FQ YAL+P ++V +NI FG+K + A + Sbjct: 59 RISINGRLLSGPETFVPSERREVGMIFQDYALFPHLTVAENILFGVK--GLDKAARQARL 116 Query: 117 ARVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRT 176 + L+++E L R P +LSGGQQQRV++ RALA P++ L DEP SN+DAK+R EM Sbjct: 117 GEMLALVKLEGLGGRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMV 176 Query: 177 EMKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFI 236 E++ + ++ + V+VTH + EA DK+A+ KDG I Q+G+ + +Y P + +VA F+ Sbjct: 177 EIREILKQRGVSAVFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFL 236 Query: 237 GSPPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANG 296 G +N++ ++ + RL LL Q+ +LP + AG L +RPEQ+ +A G Sbjct: 237 GQ--VNYLSCEVKDR-ARLQTLLGEVQSSSDLP---KAAGYRGE---LLLRPEQLQMA-G 286 Query: 297 EANGLPTIRA 306 + G TI A Sbjct: 287 DEQGEGTIIA 296 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: 303 Number of extensions: 12 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: 342 Length adjustment: 29 Effective length of query: 357 Effective length of database: 313 Effective search space: 111741 Effective search space used: 111741 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