Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate HSERO_RS18940 HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__HerbieS:HSERO_RS18940 Length = 364 Score = 311 bits (798), Expect = 1e-89 Identities = 168/363 (46%), Positives = 232/363 (63%), Gaps = 26/363 (7%) Query: 1 MAKIQFSNIKKSFGSA----DVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESAD 56 MA I ++K++G+ DV+ GID +IA GEF+V+VGPSGCGKSTLLR +AGLE Sbjct: 1 MAAIHLKQVRKTYGAGTKAVDVIHGIDAEIADGEFIVMVGPSGCGKSTLLRMVAGLEEIS 60 Query: 57 SGTISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNE 116 SG I I + +ND+EP+ RDIAMVFQ+YALYPHMTV +NM +GLK++ L+ +EI RV Sbjct: 61 SGQIVIGDRVVNDLEPKERDIAMVFQNYALYPHMTVYQNMAYGLKIQGLSKSEIDARVQR 120 Query: 117 ISELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEI 176 + +L++ LL+R P++LSGGQRQRVA+GRA+ R+ V LFDEPLSNLDA LR QMRLEI Sbjct: 121 AAAILELGALLERTPRQLSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEI 180 Query: 177 KRLHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGS 236 ++LH + ++T +YVTHDQ+EA TLG R+ V+ GV EQIGTP+E+Y RP TF+A+FIGS Sbjct: 181 QKLHASLRTTSLYVTHDQVEAMTLGQRMIVMNRGVAEQIGTPAEVYARPATTFVASFIGS 240 Query: 237 PEMNFLEGAV----------------LEKIPWPEARKADQ--ILGIRPDAFALNQGPLGT 278 P MN L+G + + ++P P A Q ILG+RP+ P+ Sbjct: 241 PPMNLLQGKLSADGASFEVSKGNASDILRLPQPLTGAAGQERILGVRPEHLL----PILD 296 Query: 279 QEVALGDFQIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFD 338 A ++++ E LG + ++H G + + + Q + H FD Sbjct: 297 GSAAQLSLEVELVEALGAELLVHARCGGQALVLRCPANVQVRTGQRIGASFGAGDVHWFD 356 Query: 339 KKT 341 K+ Sbjct: 357 VKS 359 Lambda K H 0.318 0.136 0.383 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: 338 Number of extensions: 16 Number of successful extensions: 1 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: 347 Length of database: 364 Length adjustment: 29 Effective length of query: 318 Effective length of database: 335 Effective search space: 106530 Effective search space used: 106530 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 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