Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_101443649.1 BD749_RS06040 ABC transporter ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >NCBI__GCF_002846395.1:WP_101443649.1 Length = 317 Score = 141 bits (356), Expect = 2e-38 Identities = 105/310 (33%), Positives = 151/310 (48%), Gaps = 30/310 (9%) Query: 23 VLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIRIGGKNVVG----MPPR 78 VL + E L + G +G GKSTLL IAGL +P+ G+I GK V+G + P Sbjct: 8 VLHGISFRQGEYEKLAIAGETGSGKSTLLQAIAGLVQPSAGQITFEGKRVIGPHDKLVPG 67 Query: 79 DRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAMLQISHLLDRRPSQ 138 IA + Q Y L L V + +A + + + + + EV +ISHL R+ Q Sbjct: 68 HEGIAYLSQHYDLPQFLRVEQVLRYA----NILQGDEAETLYEVC---RISHLKQRKTHQ 120 Query: 139 LSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQASGITSVYVTHD 198 LSGG+RQR+A+ R L+ P L L DEP SNLD + ++ I + + IT + ++HD Sbjct: 121 LSGGERQRIALARLLSTWPSLLLLDEPYSNLDKGHKELLKEVIHDITERLAITCILISHD 180 Query: 199 QVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTMNLLRGAVT---GGQ 255 + ++ RI ++KGG + Q GTP+++Y P + Y A G+ NL+ V + Sbjct: 181 PHDTLSWADRILIIKGGRMVQQGTPEQVYRHPVDAYTAGLFGN--YNLIPAHVALPFAEK 238 Query: 256 FGIQGAALNLAPPPSSANEVLLGVRPEH--LVMQETAPWRGRVSVVEPTGPDTYVMVDTA 313 GI A +L VRPEH V +E G V V G V V Sbjct: 239 LGIAVTARDLL------------VRPEHFRFVAKEAGSLNGTVQKVTFFGGYYDVQVQVT 286 Query: 314 AGSVTLRTDA 323 SVT+RT A Sbjct: 287 GFSVTVRTQA 296 Lambda K H 0.318 0.135 0.388 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: 251 Number of extensions: 7 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: 355 Length of database: 317 Length adjustment: 28 Effective length of query: 327 Effective length of database: 289 Effective search space: 94503 Effective search space used: 94503 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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