Align ABC transporter for Lactose, ATPase component (characterized)
to candidate AO356_05180 AO356_05180 sugar ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05180 Length = 386 Score = 310 bits (793), Expect = 5e-89 Identities = 174/368 (47%), Positives = 243/368 (66%), Gaps = 15/368 (4%) Query: 1 MSELQLSDVRKSYG-GL-EVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSG 58 M+ L+L +V K+YG GL + +K ++L IK GEF++ VGPSGCGKSTL+ IAGLE I+ G Sbjct: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKDGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 Query: 59 DLTIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAA 118 + I D ++ + P R IAMVFQSYALYP M+VREN+ F L+ + ++ I++ VN A Sbjct: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMNQSAIDEEVNRVA 120 Query: 119 HILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIAR 178 +L++ LL+RKP QLSGGQ+QRVA+GRA+ R PKI+LFDEPLSNLDA+LRV MR E+ Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 179 LHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPK 238 +H++L TT VYVTHDQ+EAMTL DK+ VM+ G+++Q G+P D+Y +PANLFVA FIGSP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFIGSPP 240 Query: 239 MNFLKGVIEIDEDQAYARLPDYGDAK--IPVTLQAAA--GTAVTIGIRPEHFDEAGP--- 291 MNF+ ++ + + A L D G A+ +P+ +Q A V +G+RPE AG Sbjct: 241 MNFIPLRLQRKDGRLLALL-DSGQARCELPMGMQDAGLEDREVILGMRPEQIMLAGSEPN 299 Query: 292 --AALDLAIDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVF 349 + + + E G +T + N + + G+ LT +FDP VL+F Sbjct: 300 GLPTIRAEVQVTEPTGPDTLVFVSL--NDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLF 357 Query: 350 DGE-GKRL 356 D + G+RL Sbjct: 358 DAQSGERL 365 Lambda K H 0.321 0.139 0.396 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: 391 Number of extensions: 14 Number of successful extensions: 2 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: 358 Length of database: 386 Length adjustment: 30 Effective length of query: 328 Effective length of database: 356 Effective search space: 116768 Effective search space used: 116768 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: 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