Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Pedo557:CA265_RS10520 Length = 568 Score = 155 bits (393), Expect = 2e-42 Identities = 97/265 (36%), Positives = 154/265 (58%), Gaps = 9/265 (3%) Query: 10 NVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGK 69 N+ Y + EK KAV +SF++ + V+G+VGESG GK+ S I + + G+ Sbjct: 8 NIDFYNQEEKTWFKAVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDERAAKITGE 67 Query: 70 IFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHG-I 128 I + E + L +++ +E+ R+ G +I++I Q M +L P V H + Sbjct: 68 I----DFEDISLLNLSSNEI-RQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHRKV 122 Query: 129 DEEELLDKARRRFEEVGLD--PLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTS 186 D+ E F EV L + YP ++SGG +QR +IA+A +P LLIADEPT+ Sbjct: 123 DQAEAKKHTIALFNEVQLPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTT 182 Query: 187 ALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESL 246 ALDV QK +L++L+++K++ + ++IFI+HD+ V +IAD + +MY G+IVE P +S+ Sbjct: 183 ALDVTVQKTILQLLLKLKQERNM-AMIFISHDLGVVNEIADEVAVMYKGEIVEQGPAKSI 241 Query: 247 LEKPLHPYTQGLFNSVLTPEPEVKK 271 E P HPYT+GL +P ++KK Sbjct: 242 FENPQHPYTKGLLACRPSPNRQLKK 266 Score = 134 bits (337), Expect = 5e-36 Identities = 95/270 (35%), Positives = 142/270 (52%), Gaps = 20/270 (7%) Query: 2 KEILLKAENVRAYYKLEKVS-------VKAVDGLSFEILEDEVIGVVGESGCGKTTLSNV 54 +E LL+ +N+ +Y + VKAVD L+FE+ E +G+VGESGCGKTTL Sbjct: 306 QEPLLQIKNLCTWYPIHNGLFGKTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGRT 365 Query: 55 IFMNMVKPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIR 114 I + +++P + G+I NGE + T RK +I II Q +L P + Sbjct: 366 I-LRLIQPTS---GEIIF--NGENITHIGKTALRKLRK----DIQIIFQDPYASLNPKLS 415 Query: 115 MEKYVRHLAESHGI--DEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIAT 172 + + + + H + ++ E K ++VGL RYP E SGG RQR VIA A Sbjct: 416 IGQSILEPLQVHKLYRNDSERKQKVLELLDKVGLKEEHFNRYPHEFSGGQRQRVVIARAL 475 Query: 173 ILNPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIM 232 L P +I DE SALDV Q +L ++ ++ + + IFI+HD+A V+ I+DR+++M Sbjct: 476 ALQPKFIICDESVSALDVSVQAQVLNLIKDLQSE-FGLTYIFISHDLAVVKHISDRILVM 534 Query: 233 YAGKIVEFAPVESLLEKPLHPYTQGLFNSV 262 GKI E E + P YTQ L ++ Sbjct: 535 NKGKIEEEGFPEQIFYAPKAAYTQKLIEAI 564 Lambda K H 0.321 0.138 0.405 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: 470 Number of extensions: 25 Number of successful extensions: 6 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: 330 Length of database: 568 Length adjustment: 32 Effective length of query: 298 Effective length of database: 536 Effective search space: 159728 Effective search space used: 159728 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