Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__HerbieS:HSERO_RS18940 Length = 364 Score = 357 bits (915), Expect = e-103 Identities = 192/374 (51%), Positives = 252/374 (67%), Gaps = 14/374 (3%) Query: 1 MARVLLEHIYKTYPGQTEPT--VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDIT 58 MA + L+ + KTY T+ + + +I D EF V VGPSGCGK+T LRM+AGLE+I+ Sbjct: 1 MAAIHLKQVRKTYGAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEIS 60 Query: 59 EGNLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQE 118 G + IGDR VND+ PK+RDIAMVFQNYALYPHMTVYQNMA+GLK++ + K+EID RVQ Sbjct: 61 SGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQR 120 Query: 119 AAKILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEI 178 AA IL++ LL+R P+ LSGGQRQRVA+GRAIVR+P VFL DEPLSNLDAKLRVQMR EI Sbjct: 121 AAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEI 180 Query: 179 RKLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGS 238 +KLH L+TT +YVTHDQ EAMT+G R++VM GV +Q TP VY++P FVA FIGS Sbjct: 181 QKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIGS 240 Query: 239 PAMNFIRGEIVQDGDAFYFRAPSIS--LRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDE 296 P MN ++G++ DG +F + S LRLP+ +GA G+ +LGVRPE L Sbjct: 241 PPMNLLQGKLSADGASFEVSKGNASDILRLPQ------PLTGAAGQERILGVRPEHL--- 291 Query: 297 EVFMTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLN 356 + + + L ++VE+VE +G+E+ +H G +V R G + + Sbjct: 292 -LPILDGSAAQLSLEVELVEALGAELLVHARCGGQALVLRCPANVQVRTGQRIGASFGAG 350 Query: 357 KIHIFDAETEESIG 370 +H FD ++ IG Sbjct: 351 DVHWFDVKSTRRIG 364 Lambda K H 0.321 0.138 0.395 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: 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: 384 Length of database: 364 Length adjustment: 30 Effective length of query: 354 Effective length of database: 334 Effective search space: 118236 Effective search space used: 118236 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