Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate AO356_05180 AO356_05180 sugar ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05180 Length = 386 Score = 352 bits (903), Expect = e-102 Identities = 186/366 (50%), Positives = 250/366 (68%), Gaps = 10/366 (2%) Query: 1 MSALEIRNIRKRYGE--VETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGG 58 M+ LE+RN+ K YG +TLK I+++++ GEFL+L+G SGCGKSTL+N IAGL +GG Sbjct: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKDGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 Query: 59 DILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTA 118 I+IG++ V G+ PKDRDIAMVFQSYALYP +SV NI FGL++R++ Q+ D+ V A Sbjct: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMNQSAIDEEVNRVA 120 Query: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKR 178 +LLQIE+LL+RKP QLSGGQ+QRVA+GRAL R P+++LFDEPLSNLDAKLR+EMRTE+K Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 179 LHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPP 238 +HQ L+TT VYVTHDQIEAMTL ++AVM+DG I+Q P ++Y PA L+VA F+GSPP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFIGSPP 240 Query: 239 MNILDAEMTANGLK----IEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQ 294 MN + + + ++ + LP A R V +G+RPE + L AGSE Sbjct: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPMGMQDAGLEDREVILGMRPEQIML-AGSEPN 299 Query: 295 RL---TASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDP 351 L A V+V E TGP+ + ++ ++ L P A +G FD + + LFD Sbjct: 300 GLPTIRAEVQVTEPTGPDTLVFVSLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDA 359 Query: 352 ESGRSL 357 +SG L Sbjct: 360 QSGERL 365 Lambda K H 0.320 0.136 0.385 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: 402 Number of extensions: 11 Number of successful extensions: 4 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: 360 Length of database: 386 Length adjustment: 30 Effective length of query: 330 Effective length of database: 356 Effective search space: 117480 Effective search space used: 117480 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 (21.8 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