Align MalG, component of Maltose and maltooligosaccharide porter (characterized)
to candidate AZOBR_RS02620 AZOBR_RS02620 D-ala-D-ala transporter subunit
Query= TCDB::Q97UG3 (323 letters) >FitnessBrowser__azobra:AZOBR_RS02620 Length = 306 Score = 105 bits (263), Expect = 1e-27 Identities = 87/291 (29%), Positives = 137/291 (47%), Gaps = 38/291 (13%) Query: 13 ALFNNKFILAGIVIILVDFAIGIVGAFWTPY-PVSETFGISL-PPSSAHILGTDEFGHDV 70 A N+ + G+ I+L+ + + PY P ++ L PPS+AH LGTD FG D+ Sbjct: 38 AFARNRLAMIGLGIVLLLVLMAALAPLLAPYDPYTQDLSQRLLPPSAAHWLGTDAFGRDI 97 Query: 71 LS-VMMASTLTSLIVGISVGALIAIISTLIGLFGGYYGGKISGVIIDILTITALTIPGVI 129 LS ++ S LT +IV + V + LIG GY GG + V++ + I L P +I Sbjct: 98 LSRILYGSRLTLMIVAL-VAVTAPVAGLLIGTVAGYLGGWVDAVLMRVTDI-FLAFPKLI 155 Query: 130 LLVIIEAYFRAASSTINITLSYIIVVIGLAITSWAFGAKQIRAQVLSISKRDYIIASRLI 189 L + A+ A I +I +AITSW A+ RA+ ++I K D+I A+RL Sbjct: 156 LAL---AFVSALGPGIE------NAIIAIAITSWPPYARIARAETITIRKSDFISAARLQ 206 Query: 190 GEKSWRIIFNQILP---SILPLTVAQFLFGVL--------YGILSLITAEFWGVLPTNIN 238 G + RII ++P S L + V + G++ G+ + A WG + Sbjct: 207 GASTPRIILGHVVPLCSSSLIVRVTLDMAGIILTAAGLGFLGLGAQPPAPEWGAM----- 261 Query: 239 NLGTMLFFISSNGAYLSNQWWWILGAIIPIMVLGAGLGILNIGIDEFIDPR 289 I++ Y+ QWW I I V+ G +L G+ + +DP+ Sbjct: 262 --------IATGRQYVLEQWWVATMPGIAIFVVSLGFNLLGDGLRDVLDPK 304 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: 254 Number of extensions: 18 Number of successful extensions: 3 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: 306 Length adjustment: 27 Effective length of query: 296 Effective length of database: 279 Effective search space: 82584 Effective search space used: 82584 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