Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate GFF3011 HP15_2955 ATP-binding component of ABC transporter
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Marino:GFF3011 Length = 372 Score = 432 bits (1111), Expect = e-126 Identities = 225/369 (60%), Positives = 277/369 (75%), Gaps = 4/369 (1%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 M+ LELR++ KTY +TLK I++ I GEFLILVGPSGCGKSTLMN IAGLETI+ G Sbjct: 1 MSQLELRSIRKTYPGVAEETLKGIDIDIASGEFLILVGPSGCGKSTLMNTIAGLETITDG 60 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 +I++D DIS M PKDRDIAMVFQSYALYPTMSVR+NIAFGLKIR +P EID+EV RV+ Sbjct: 61 SIVLDGKDISTMEPKDRDIAMVFQSYALYPTMSVRENIAFGLKIRGLPKHEIDQEVERVA 120 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 LLQI L+++KP LSGGQQQRVAMGRALARRP+IYLFDEPLSNLDAKLRVEMRTE+K Sbjct: 121 DLLQISPLMNKKPANLSGGQQQRVAMGRALARRPRIYLFDEPLSNLDAKLRVEMRTEIKK 180 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 +HQRLKTT VYVTHDQIEAMTL D++AV+KDG +QQ GTPK++Y+ P NLFVA F+GSP Sbjct: 181 LHQRLKTTIVYVTHDQIEAMTLADRIAVLKDGELQQLGTPKEVYDRPENLFVAGFMGSPA 240 Query: 241 MNFIPLRLQRKDGRLLALLDSGQAR-CELPLGMQDAGLEDREVILGIRPEQIILANGEAN 299 M+F+P+ +++ +G L A + R +LP+ A ++VILGIRPE I + N Sbjct: 241 MSFVPVTVEQGEGGLQAEVRGNDGRSVKLPVPEFLADRVGKKVILGIRPEHITQPQDQKN 300 Query: 300 GLPTI---RAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLL 356 + ++VTEPTGPD + + LNDT V CR+ P+ GET L FD KV+ Sbjct: 301 DQTLVAKGEFTIEVTEPTGPDVIALIQLNDTNVHCRIDPEHPVTWGETAELMFDMKKVVF 360 Query: 357 FDAKTGERL 365 FD +T +R+ Sbjct: 361 FDPETEKRI 369 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: 485 Number of extensions: 18 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: 372 Length adjustment: 30 Effective length of query: 356 Effective length of database: 342 Effective search space: 121752 Effective search space used: 121752 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