Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate AZOBR_RS31020 AZOBR_RS31020 methionine ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__azobra:AZOBR_RS31020 Length = 329 Score = 191 bits (485), Expect = 2e-53 Identities = 106/285 (37%), Positives = 169/285 (59%), Gaps = 4/285 (1%) Query: 63 IKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIFSMT 122 +KAV+ V +++GEILG++GESGSGK+ +IL + PPG+++ G+V+F G D+ Sbjct: 22 VKAVDGVDLRLDRGEILGLVGESGSGKSVTGQSILGLVDPPGQVVGGRVLFQGEDLVGAG 81 Query: 123 IDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIERASELLKLVG 182 R + + I+ + Q LNPVL I +H + + ER+ L VG Sbjct: 82 EKRLRAIRGRRIAMIFQDPMMTLNPVLSIGTQMVEAVRAHDKVSRAEAWERSRRALARVG 141 Query: 183 L-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLIKNI 241 + P L YP Q SGGM+QRV IA++LL +P LI+ DEPT+ALD+ Q +L ++ + Sbjct: 142 IASPDERLASYPHQFSGGMRQRVAIAIALLHSPDLIIADEPTTALDVTIQAQILFEVQTL 201 Query: 242 NQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSSIPS 301 +E G +++VTHD+ ++ +A+R+ VMY G V+E G EII +P +PYT L+ S+PS Sbjct: 202 CRETGTALIWVTHDLAVVSALADRVAVMYAGRVVETGTVAEIIGNPRHPYTRGLLESVPS 261 Query: 302 L-KGEVKVINVP-LDEPLVSKEKGCPFLARCSKAFGRCKEELPEI 344 + V + ++P + ++ +GC F RC ++ G C +PE+ Sbjct: 262 RNRRGVPLRSIPGMTPSVLDLPEGCAFRPRCDRSTGAC-TVMPEL 305 Lambda K H 0.319 0.138 0.391 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: 220 Number of extensions: 8 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: 362 Length of database: 329 Length adjustment: 29 Effective length of query: 333 Effective length of database: 300 Effective search space: 99900 Effective search space used: 99900 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