Align MalG, component of Maltose and maltooligosaccharide porter (characterized)
to candidate AZOBR_RS23925 AZOBR_RS23925 peptide ABC transporter permease
Query= TCDB::Q97UG3 (323 letters) >FitnessBrowser__azobra:AZOBR_RS23925 Length = 295 Score = 111 bits (277), Expect = 2e-29 Identities = 87/291 (29%), Positives = 142/291 (48%), Gaps = 24/291 (8%) Query: 15 FNNKFILAGIVIILVDFAIGIVGAFWTPYPVSET--FGISLPPSSAHILGTDEFGHDVLS 72 F + L G++++ + + + + P ET PPS+AH+LGTD+FG DVLS Sbjct: 22 FRHPGFLIGVILLTLLLIVAVAAPWIAPMSPLETDLANTLAPPSAAHLLGTDQFGRDVLS 81 Query: 73 VMMASTLTSLIVGISVGALIAIISTLIGLFGGYYGGKISGVIIDILTITALTIPGVILLV 132 ++ T SL V ++V AL + +IG G++GG + V + I+ I L PG +L + Sbjct: 82 RLIWGTRISLQVAVAVMALSLSLGMVIGAVAGFFGGWVERVTVSIIDI-LLAFPGFLLAL 140 Query: 133 IIEAYFRAASSTINITLSYIIVVIGLAITSWAFGAKQIRAQVLSISKRDYIIASRLIGEK 192 + A A S +L +I+ + LA T A +RA VL+I R Y+ ASR IG Sbjct: 141 ALVA---ARGS----SLESVIIAVALAFTPRV--AAVMRAVVLTIKPRTYVEASRAIGMG 191 Query: 193 SWRIIFNQILPSILPLTVAQFLFGVLYGILSLITAEFWGV-----LPTNINNLGTMLFFI 247 + R++F ++P+ LP + IL+ F G+ PT N + F+ Sbjct: 192 TMRLLFLHVVPNSLPPVIVVATVSAATAILAEAGLSFLGLGVQPPAPTWGNVIADGQSFL 251 Query: 248 SSNGAYLSNQWWWILGAIIPIMVLGAGLGILNIGIDEFIDPRLKEVKPKVI 298 +SN L A I I V+ L +L G+ + +DP+++ +V+ Sbjct: 252 ASNPLI-------SLSAGICIAVMVVALNLLGDGLRDTLDPQMRRSSGRVL 295 Lambda K H 0.326 0.144 0.427 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: 197 Number of extensions: 10 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: 323 Length of database: 295 Length adjustment: 27 Effective length of query: 296 Effective length of database: 268 Effective search space: 79328 Effective search space used: 79328 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 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