Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate GFF3769 PGA1_262p01730 putative glutathione import ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Phaeo:GFF3769 Length = 325 Score = 201 bits (511), Expect = 2e-56 Identities = 122/317 (38%), Positives = 182/317 (57%), Gaps = 8/317 (2%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +LE+ +L+V Y+ + KA+ +SF V KGEI+GI+GESG GK+TLISAILR I P Sbjct: 5 LLEIDDLSVDYETARGDL-KALRSISFDVNKGEIVGIVGESGCGKSTLISAILRLIAPNT 63 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISH-G 163 + +G+V F G D+ + R L DIS V Q NPV+ I + I H Sbjct: 64 RFRNGEVRFKGEDLLVASDRHIRDLRGDDISIVFQDPMQTHNPVISIGKQMVD--IQHRS 121 Query: 164 EADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEP 222 +A K + A+++L VG+ DP LK YP + SGGM+QR+ IA++L+ P L++ DEP Sbjct: 122 KASKAEKLATAAKMLGAVGIPDPEMRLKQYPHEFSGGMRQRIAIAMALMSEPDLLIADEP 181 Query: 223 TSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEE 282 T+ALD + +++ +K + E G I++++H + IA++ +R++VMY G V+E G E Sbjct: 182 TTALDATLEVQIIERLKELQSEFGCAILFISHHLGVIAELCDRVVVMYAGAVVESGTVRE 241 Query: 283 IIKSPLNPYTSLLVSSIPS-LKGEVKVI-NVPLDEP-LVSKEKGCPFLARCSKAFGRCKE 339 I +P +PYT L+ P LK +V+ +P + P L + +GC F RC +A RC Sbjct: 242 IFHNPKHPYTRRLIECDPGHLKERARVLPTIPGEVPDLANLPEGCIFRDRCDQAMDRCAS 301 Query: 340 ELPEIRLVYDRKVRCHL 356 P RL C L Sbjct: 302 VPPLARLSEGHNAACWL 318 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: 262 Number of extensions: 7 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: 325 Length adjustment: 29 Effective length of query: 333 Effective length of database: 296 Effective search space: 98568 Effective search space used: 98568 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