Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate WP_034411801.1 H566_RS0113525 polyamine ABC transporter ATP-binding protein
Query= TCDB::Q88P35 (384 letters) >NCBI__GCF_000482785.1:WP_034411801.1 Length = 372 Score = 224 bits (571), Expect = 3e-63 Identities = 124/290 (42%), Positives = 175/290 (60%), Gaps = 5/290 (1%) Query: 23 DIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGGAILIDEQDVSGMSPKDRDIAMV 82 D+ LSI+ GE L+G SGCGKSTL+ +AG E T G IL++ +D+S + P +R I M+ Sbjct: 34 DVSLSIRKGEIFALLGSSGCGKSTLLRMLAGFEAPTAGHILLENRDISALPPYERPINMM 93 Query: 83 FQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVAKLLQIEHLLARKPAQLSGGQQQ 142 FQSYAL+P ++V ENI FGLK LP+ I E V + L+Q+ RKP QLSGGQQQ Sbjct: 94 FQSYALFPHLTVWENIAFGLKRDGLPKTEIAERVEAMLSLVQLNKFAKRKPHQLSGGQQQ 153 Query: 143 RVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQIEAMTL 202 RVA+ R+LA++P++ L DEPL LD KLR + + E+ + +++ T V VTHDQ EAMT+ Sbjct: 154 RVALARSLAKKPRLLLLDEPLGALDKKLREQTQLELVNIIKQVGVTCVMVTHDQEEAMTM 213 Query: 203 GDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIGSPPMNFIPVRLARQDGRLLALLDSG 262 D++A+M G Q G P +IY PAN+FVA FIG+ +N L + + + Sbjct: 214 ADRIAIMSAGSFLQVGQPHEIYETPANRFVADFIGN--VNLFDGTLVVDEPDHVVI---N 268 Query: 263 QARCELPLGEAADALEGREIILGIRPEQIALGAADGNGLPAIRAEVQVTE 312 +C + G + + +RPE+IALG + AEV V + Sbjct: 269 TPQCGFYVSHGITGTVGMPVTVALRPEKIALGRDRPDSTEHNCAEVTVAD 318 Lambda K H 0.320 0.137 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: 335 Number of extensions: 12 Number of successful extensions: 2 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: 384 Length of database: 372 Length adjustment: 30 Effective length of query: 354 Effective length of database: 342 Effective search space: 121068 Effective search space used: 121068 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: 50 (23.9 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