Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_028310092.1 H566_RS0101920 ABC transporter ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >NCBI__GCF_000482785.1:WP_028310092.1 Length = 338 Score = 229 bits (584), Expect = 8e-65 Identities = 136/347 (39%), Positives = 201/347 (57%), Gaps = 21/347 (6%) Query: 2 ASSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPT 61 AS +++ ++K +G ++V+ +D+ +A G + L+GPSGCGK++ L +IAG +E + Sbjct: 4 ASDIELVKVSKLYGGSTRAVDA---IDLRIAAGSYCCLLGPSGCGKTSTLRMIAGHEEAS 60 Query: 62 EGEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDE 121 +G+I IGG NV +PP +R AM+FQSYAL+P +S DN+ ++L++R K R+KR E Sbjct: 61 DGDIIIGGHNVTLLPPSERGTAMMFQSYALFPHMSAIDNVAYSLKVRGQDKVTRRKRAAE 120 Query: 122 VAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEI 181 V ++ ++ +R+P+QLSGGQ+QRVA+ RAL +P++ L DEPLS LD LRV+MRAE+ Sbjct: 121 VLELVSMTPYAERKPAQLSGGQQQRVALARALVNEPRVLLLDEPLSALDPFLRVKMRAEL 180 Query: 182 KRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGS 241 KR + GIT V+VTH Q EAM L VM G ++Q G+P +I+NRP +VA F+ Sbjct: 181 KRWQKDLGITFVHVTHSQEEAMALSDLAVVMSHGRIEQAGSPHDIFNRPRTEFVARFL-- 238 Query: 242 PTMNLLRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQETAPWRGRVSVVEP 301 GG I+ A AP A++V L + + G V VE Sbjct: 239 -----------GGHNVIRADAGRPAPIAVRADKVKLAAGAPATAGFDGSSIAGLVRGVEY 287 Query: 302 TGPDTYVMVDTAAGS--VTLRTDAQ---TRVQPGEHVGLALAPAHAH 343 G V +D A V + +A +QPGE L+ A AH Sbjct: 288 QGVHVLVTLDAAGDQELVAMVDEASYYAAPLQPGEACTLSWNSADAH 334 Lambda K H 0.318 0.135 0.388 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: 270 Number of extensions: 7 Number of successful extensions: 1 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: 355 Length of database: 338 Length adjustment: 29 Effective length of query: 326 Effective length of database: 309 Effective search space: 100734 Effective search space used: 100734 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 (21.7 bits) S2: 49 (23.5 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