Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_086508118.1 BZY95_RS00870 ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >NCBI__GCF_002151265.1:WP_086508118.1 Length = 766 Score = 236 bits (603), Expect = 1e-66 Identities = 121/314 (38%), Positives = 198/314 (63%), Gaps = 5/314 (1%) Query: 45 ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104 +L+V +L + Y G + +AV+ + F + GE LG++GESG GKTT A+LR + P G Sbjct: 6 LLKVEDLAIHYRTGAGPV-QAVDGIHFDLRPGEALGLVGESGCGKTTAAKAMLRLLPPNG 64 Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGE 164 ++ G++ F+G D+ ++ + RK+ WK+I+++ QA+ NAL+PV + + +H + Sbjct: 65 EVPRGRIDFDGRDLVALDEESMRKVRWKEIAWISQAAMNALDPVYTVGDQILEAMNAHIK 124 Query: 165 ADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTS 224 D+K A EL + VG+DP R L YP ++SGGMKQR +IA++L L+PKLI+ DEPT+ Sbjct: 125 IDRKTAWAHAEELFRAVGIDPGR-LSAYPHEMSGGMKQRAVIAMALALDPKLIIADEPTT 183 Query: 225 ALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEII 284 ALD++ Q +L + + +E G+ ++++THDI + Q +R+ VMY G++ME G E+ Sbjct: 184 ALDVVTQAQILARLSKLRRERGMGLLFITHDISVVVQTCDRVAVMYGGHIMETGPVREVF 243 Query: 285 KSPLNPYTSLLVSSIPSLKG-EVKVINVPLDEP-LVSKEKGCPFLARCSKAFGRCKEELP 342 +P +PYT L ++ P+L+G + ++I++P P L++ GC F RC A RC E P Sbjct: 244 GTPFHPYTMGLTNAFPTLEGAQRELISIPGSPPDLLNPPSGCRFAERCPFATERCVRETP 303 Query: 343 EIRLV-YDRKVRCH 355 + V +R+ CH Sbjct: 304 PLHPVGEERQAACH 317 Score = 165 bits (418), Expect = 3e-45 Identities = 99/293 (33%), Positives = 158/293 (53%), Gaps = 13/293 (4%) Query: 51 LNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGK 110 L+ + R + AV+ +SF + +GEILG+ GESGSGKTT ++R + + G+ Sbjct: 379 LDGLRGRNKDRKVHAVDGISFDLREGEILGLAGESGSGKTTTGEMLVRLL----DVTEGE 434 Query: 111 VIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRV 170 + F G DI +T E K + + Q LNP I +I I H A+ + + Sbjct: 435 IRFEGADIAQLTGREL-KTFRRRAQMIFQDPYQTLNPRFTIFDIVAEPLIIHRLAEGEAL 493 Query: 171 IERASELLKLVGLDPARVL-KMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDML 229 ++ L+ GL PA V + +P +LSGG +QRV IA +++L P+ I+ DEP S LD+ Sbjct: 494 RQKVVVALERAGLKPAEVYAERFPHELSGGQRQRVAIARAIVLEPRFIVADEPVSMLDVS 553 Query: 230 NQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLN 289 + +L L+ E+G++ VYV+HD+ I +A+R +MY G ++E G TE++++ + Sbjct: 554 IRAGVLNLMHRFRNELGISFVYVSHDLPTIRYVADRTAIMYLGEIVEVGPTEQVVRERKH 613 Query: 290 PYTSLLVSSIPSLKGEVKVINVPLDE-----PLVSKEKGCPFLARCSKAFGRC 337 PYT LL+ + P + + V+ PL+ V GC F RC +A C Sbjct: 614 PYTQLLLEASP--EPDPAVVKPPLESAGEIPSAVEPPNGCHFHTRCPRAMAHC 664 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: 572 Number of extensions: 22 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 362 Length of database: 766 Length adjustment: 35 Effective length of query: 327 Effective length of database: 731 Effective search space: 239037 Effective search space used: 239037 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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