Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate CA265_RS10520 CA265_RS10520 ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Pedo557:CA265_RS10520 Length = 568 Score = 266 bits (680), Expect = 9e-76 Identities = 132/259 (50%), Positives = 193/259 (74%), Gaps = 8/259 (3%) Query: 11 KPLLQTVDLKKYFPQGKRI-------LKAVDGISIEIKEGETLGLVGESGCGKSTLGRTI 63 +PLLQ +L ++P + +KAVD ++ E+ GETLGLVGESGCGK+TLGRTI Sbjct: 307 EPLLQIKNLCTWYPIHNGLFGKTTDYVKAVDQLNFEVFPGETLGLVGESGCGKTTLGRTI 366 Query: 64 LKLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLII 123 L+L++P G+I F G++IT++ ++ RK +QIIFQDP SLNP++++G+ I +PL + Sbjct: 367 LRLIQPTSGEIIFNGENITHIGKTALRKLRKDIQIIFQDPYASLNPKLSIGQSILEPLQV 426 Query: 124 HKI-GTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDE 182 HK+ ER+++V ELLD VG+ E N +PHEFSGGQ+QR+ IARALAL PKFI+CDE Sbjct: 427 HKLYRNDSERKQKVLELLDKVGLKEEHFNRYPHEFSGGQRQRVVIARALALQPKFIICDE 486 Query: 183 PVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVD 242 VSALDVS+QAQ+++L++++Q + G++Y+FI+H+LAVV+HIS ++ VM GKI E G + Sbjct: 487 SVSALDVSVQAQVLNLIKDLQSEFGLTYIFISHDLAVVKHISDRILVMNKGKIEEEGFPE 546 Query: 243 KIFLNPIHPYTRALLKSVP 261 +IF P YT+ L++++P Sbjct: 547 QIFYAPKAAYTQKLIEAIP 565 Score = 182 bits (462), Expect = 2e-50 Identities = 100/255 (39%), Positives = 159/255 (62%), Gaps = 7/255 (2%) Query: 14 LQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG-- 71 ++ +++ Y + K KAV IS ++K+G LG+VGESG GKS +I++L Sbjct: 4 VEHLNIDFYNQEEKTWFKAVKQISFKVKKGTVLGIVGESGSGKSVTSFSIMRLHDERAAK 63 Query: 72 --GKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGT 128 G+I FE + NL+ E++ R ++ +IFQ+P+ SLNP T G + + +++H+ Sbjct: 64 ITGEIDFEDISLLNLSSNEIRQIRGNQISMIFQEPMTSLNPVFTCGYQVAEAIMLHRKVD 123 Query: 129 KKERRKRVEELLDMVGIGR--EFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSA 186 + E +K L + V + R + S+PH+ SGGQ+QR+ IA AL+ +PK ++ DEP +A Sbjct: 124 QAEAKKHTIALFNEVQLPRPEKIFESYPHQISGGQKQRVMIAMALSCDPKLLIADEPTTA 183 Query: 187 LDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFL 246 LDV++Q I+ LL +++Q+ ++ +FI+H+L VV I+ +VAVMY G+IVE G IF Sbjct: 184 LDVTVQKTILQLLLKLKQERNMAMIFISHDLGVVNEIADEVAVMYKGEIVEQGPAKSIFE 243 Query: 247 NPIHPYTRALLKSVP 261 NP HPYT+ LL P Sbjct: 244 NPQHPYTKGLLACRP 258 Lambda K H 0.321 0.142 0.417 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: 543 Number of extensions: 21 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: 328 Length of database: 568 Length adjustment: 32 Effective length of query: 296 Effective length of database: 536 Effective search space: 158656 Effective search space used: 158656 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