Align ABC transporter for Lactose, ATPase component (characterized)
to candidate HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__HerbieS:HSERO_RS18940 Length = 364 Score = 353 bits (905), Expect = e-102 Identities = 189/363 (52%), Positives = 246/363 (67%), Gaps = 10/363 (2%) Query: 1 MSELQLSDVRKSYGG----LEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEIS 56 M+ + L VRK+YG ++VI G+D +I GEF+V VGPSGCGKSTLLRM+AGLEEIS Sbjct: 1 MAAIHLKQVRKTYGAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEIS 60 Query: 57 SGDLTIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNE 116 SG + I D +ND++P +R IAMVFQ+YALYPHMTV +NM + L+ G+ ++EI+ RV Sbjct: 61 SGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQR 120 Query: 117 AAHILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEI 176 AA ILELGALL+R P+QLSGGQRQRVA+GRAIVR P +FLFDEPLSNLDA+LRV MR+EI Sbjct: 121 AAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEI 180 Query: 177 ARLHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGS 236 +LH L TT +YVTHDQVEAMTL +++VM GV EQ+G+P ++Y PA FVA FIGS Sbjct: 181 QKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIGS 240 Query: 237 PKMNFLKGVIEIDEDQAYARLPDYGD-AKIPVTLQAAAGTAVTIGIRPEH---FDEAGPA 292 P MN L+G + D + D ++P L AAG +G+RPEH + A Sbjct: 241 PPMNLLQGKLSADGASFEVSKGNASDILRLPQPLTGAAGQERILGVRPEHLLPILDGSAA 300 Query: 293 ALDLAIDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDGE 352 L L ++++E LG E +AR G+ +V+ ++TG R+ A F V FD + Sbjct: 301 QLSLEVELVEALGAELLVHAR--CGGQALVLRCPANVQVRTGQRIGASFGAGDVHWFDVK 358 Query: 353 GKR 355 R Sbjct: 359 STR 361 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: 379 Number of extensions: 14 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: 358 Length of database: 364 Length adjustment: 29 Effective length of query: 329 Effective length of database: 335 Effective search space: 110215 Effective search space used: 110215 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