Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 310 bits (793), Expect = 5e-89 Identities = 177/370 (47%), Positives = 227/370 (61%), Gaps = 45/370 (12%) Query: 1 MARVLLEHIYKTYPG--QTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDIT 58 MA + L +I K Y + + N +++D EF V VGPSGCGK+T LRM+AGLE+I+ Sbjct: 1 MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60 Query: 59 EGNLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQE 118 G L IGDR VND+ P RDIAMVFQNYALYPHMT ++NMA+GLK+ KVPK EI RV + Sbjct: 61 GGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVDK 120 Query: 119 AAKILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEI 178 AAKIL++ HLL+RKP+ LSGGQRQRVA+GRAIVR+PQVFL DEPLSNLDAKLR Q R EI Sbjct: 121 AAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLEI 180 Query: 179 RKLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGS 238 +KLH+ L T ++VTHDQ EAMT+ R++VM G ++Q TP+ VY P FVA FIGS Sbjct: 181 QKLHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVASFIGS 240 Query: 239 PAMNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPE--DLHDE 296 P MN +LK + +LG+RPE D+ E Sbjct: 241 PPMN------------------------------LLKNAPGAQPGTILGIRPEHLDVRSE 270 Query: 297 EVFMTTYPDSVLQMQVEVVEHMGSEVYLHTSIGPNTIVARVNP-RHVYHVGSSVKLAIDL 355 +T VE VE +G+E ++ I ++ RV H S + + Sbjct: 271 GWAVT----------VETVELLGAERLIYGRINGEQVIVRVEEGTHSPEPDSVIHVQPRA 320 Query: 356 NKIHIFDAET 365 +++H FDA T Sbjct: 321 DRLHAFDAAT 330 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: 377 Number of extensions: 13 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: 384 Length of database: 334 Length adjustment: 29 Effective length of query: 355 Effective length of database: 305 Effective search space: 108275 Effective search space used: 108275 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