Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_013402438.1 CALHY_RS02475 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000166355.1:WP_013402438.1 Length = 499 Score = 393 bits (1009), Expect = e-114 Identities = 208/502 (41%), Positives = 334/502 (66%), Gaps = 20/502 (3%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +L + ITK FPG AL +V+ V + EIHA+VGENGAGKSTLM ++SG +GEI Sbjct: 9 LLRLHGITKIFPGTVALSDVSFSVNKAEIHAIVGENGAGKSTLMNIISGSLLPD--KGEI 66 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGN-EVASNGVISWQQTFNR 123 + EG N R+ D++++GI I+HQELAL P L++AENI++G S ++ +++ Sbjct: 67 YLEGKKVNIRSPRDAQNLGISIVHQELALCPHLTVAENIYIGRLPEKSAKIVDFKKLNQM 126 Query: 124 TRELLK---KVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180 ++E+L +V +K P + ++ V +QQ+VEIAKA++ + KLLILDEPT++L+E+D+ Sbjct: 127 SQEVLSLFDEVNIK--PTDKVANLNVAQQQIVEIAKAITFNCKLLILDEPTSALSEADAA 184 Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240 L ++ + + +G++ + I+H+L E+ ++AD+ITVLRDG + TL+ E + D ++ Sbjct: 185 VLFKIIKDLKAKGISILYISHRLREIFELADRITVLRDGRYITTLNT--AETNPDQVVSL 242 Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300 MVGR++++ YPP+ IG + V+N ++ Q+ ++ + +GE++G AGL+G Sbjct: 243 MVGREIKEMYPPKSSKIGREVFRVENISSDKVQN--------VSFALHEGEILGFAGLVG 294 Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360 +GRTE A ++ G H G++ ++GK +++++ AI + YVTEDRK GL L Sbjct: 295 SGRTELAQTICGILPKH--CGEIYLEGKKIEINSFEDAIRHKIGYVTEDRKQYGLFLKLP 352 Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420 + HN + +L K +ID KE+ +A +F +L +++S Q ++LSGGNQQKV+++ Sbjct: 353 VAHNVSAIHLKYDYKRLLIDRQKELSLAQEFVKKLNVKTSSYVQLVMSLSGGNQQKVMIA 412 Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480 KWL P +LILDEPTRGIDVGAK EI++++ +LA +G G+++ISSE+PE++G CDR+ V Sbjct: 413 KWLAIKPRILILDEPTRGIDVGAKAEIHSLLRELAKNGIGIILISSELPEIIGMCDRVLV 472 Query: 481 MNEGRIVAELPKGEASQESIMR 502 M EGRI EL ++E+IM+ Sbjct: 473 MREGRITGELSGSSITEENIMQ 494 Lambda K H 0.316 0.135 0.374 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: 649 Number of extensions: 38 Number of successful extensions: 10 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: 512 Length of database: 499 Length adjustment: 34 Effective length of query: 478 Effective length of database: 465 Effective search space: 222270 Effective search space used: 222270 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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