Align MalG, component of Maltose and maltooligosaccharide porter (characterized)
to candidate GFF2799 PGA1_c28420 putative D,D-dipeptide transport system permease protein
Query= TCDB::Q97UG3 (323 letters) >FitnessBrowser__Phaeo:GFF2799 Length = 300 Score = 98.6 bits (244), Expect = 2e-25 Identities = 81/288 (28%), Positives = 135/288 (46%), Gaps = 24/288 (8%) Query: 9 RIRKALFNNKFILAGIVIILVDFAIGIVGAFWTPY-----PVSETFGISL-PPSSAHILG 62 R+ AL N + G VII I I+ A + P+ PV + L PPS A+ +G Sbjct: 25 RMILALMRNPLAVLGAVII----TILILAAAFAPWIAPQSPVGQDLSSRLLPPSWANWMG 80 Query: 63 TDEFGHDVLSVMMASTLTSLIVGISVGALIAIISTLIGLFGGYYGGKISGVIIDILTITA 122 TDE G D+ S ++ +L++ V + A + +IG GY+GG + +++ I T Sbjct: 81 TDELGRDIFSRVVYGARITLMIVALVAVISAPLGLIIGAIAGYFGGWVDRILMGI-TDVF 139 Query: 123 LTIPGVILLVIIEAYFRAASSTINITLSYIIVVIGLAITSWAFGAKQIRAQVLSISKRDY 182 L++P +IL + A+ A I +I +AIT+W A+ RA+ L+ ++ Sbjct: 140 LSMPKLILAL---AFVAALGPGIE------NAIIAIAITAWPAYARIARAETLTFRNAEF 190 Query: 183 IIASRLIGEKSWRIIFNQILPSILPLTVAQFLFGVLYGILSLITAEFWGV-LPTNINNLG 241 I A+RL+G R+I +LP + + + IL+ F G+ + G Sbjct: 191 IAATRLLGASHSRVILQHVLPLCTSSMIVRVTLDMAGIILTAAGLGFLGLGAQPPLPEWG 250 Query: 242 TMLFFISSNGAYLSNQWWWILGAIIPIMVLGAGLGILNIGIDEFIDPR 289 M IS ++ +QWW I I+V+ G L G+ + +DP+ Sbjct: 251 AM---ISRGRVFILDQWWVATMPGIAIIVVSLGFCFLGDGLRDVLDPK 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: 246 Number of extensions: 17 Number of successful extensions: 5 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: 300 Length adjustment: 27 Effective length of query: 296 Effective length of database: 273 Effective search space: 80808 Effective search space used: 80808 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