Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__Pedo557:CA265_RS10520 Length = 568 Score = 176 bits (445), Expect = 2e-48 Identities = 94/272 (34%), Positives = 162/272 (59%), Gaps = 2/272 (0%) Query: 45 ILEVHNLNV-IYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPP 103 +L V +LN+ Y++ KAV +SF V+KG +LGI+GESGSGK+ +I+R Sbjct: 1 MLNVEHLNIDFYNQEEKTWFKAVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDER 60 Query: 104 GKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHG 163 I+G++ F + + +++ +E R++ IS + Q +LNPV + H Sbjct: 61 AAKITGEIDFEDISLLNLSSNEIRQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHR 120 Query: 164 EADKKRVIERASELLKLVGLD-PARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEP 222 + D+ + L V L P ++ + YP Q+SGG KQRVMIA++L +PKL++ DEP Sbjct: 121 KVDQAEAKKHTIALFNEVQLPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEP 180 Query: 223 TSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEE 282 T+ALD+ Q+ +L+L+ + QE + +++++HD+ + +IA+ + VMYKG ++E+G + Sbjct: 181 TTALDVTVQKTILQLLLKLKQERNMAMIFISHDLGVVNEIADEVAVMYKGEIVEQGPAKS 240 Query: 283 IIKSPLNPYTSLLVSSIPSLKGEVKVINVPLD 314 I ++P +PYT L++ PS ++K + V D Sbjct: 241 IFENPQHPYTKGLLACRPSPNRQLKKLPVVAD 272 Score = 162 bits (410), Expect = 2e-44 Identities = 105/267 (39%), Positives = 152/267 (56%), Gaps = 21/267 (7%) Query: 45 ILEVHNLNVIYDEGNSRI------IKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILR 98 +L++ NL Y N +KAV+ ++F V GE LG++GESG GKTTL ILR Sbjct: 309 LLQIKNLCTWYPIHNGLFGKTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGRTILR 368 Query: 99 AIRPPGKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISE----- 153 I+P SG++IFNG +I + RKL KDI + Q +LNP L I + Sbjct: 369 LIQPT----SGEIIFNGENITHIGKTALRKLR-KDIQIIFQDPYASLNPKLSIGQSILEP 423 Query: 154 IFYHEAISHGEADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLN 213 + H+ + K++V+E LL VGL YP + SGG +QRV+IA +L L Sbjct: 424 LQVHKLYRNDSERKQKVLE----LLDKVGLKEEH-FNRYPHEFSGGQRQRVVIARALALQ 478 Query: 214 PKLILMDEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGY 273 PK I+ DE SALD+ Q +L LIK++ E G+T ++++HD+ + I++R+LVM KG Sbjct: 479 PKFIICDESVSALDVSVQAQVLNLIKDLQSEFGLTYIFISHDLAVVKHISDRILVMNKGK 538 Query: 274 VMEEGKTEEIIKSPLNPYTSLLVSSIP 300 + EEG E+I +P YT L+ +IP Sbjct: 539 IEEEGFPEQIFYAPKAAYTQKLIEAIP 565 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: 473 Number of extensions: 20 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: 568 Length adjustment: 33 Effective length of query: 329 Effective length of database: 535 Effective search space: 176015 Effective search space used: 176015 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: 51 (24.3 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