Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= TCDB::G3LHY8 (358 letters) >NCBI__GCF_900167125.1:WP_078717009.1 Length = 370 Score = 169 bits (427), Expect = 1e-46 Identities = 98/309 (31%), Positives = 158/309 (51%), Gaps = 5/309 (1%) Query: 1 MLELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHF 60 ++ L + AK + ++ L + G +LGP+ GKT+L+RL+AG + P+ G I Sbjct: 7 VIRLEHVAKEFDGETVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIIL 66 Query: 61 DGTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLK 120 DG + +P R V V+Q + +P ++V++N+A +R+SG I V KA ++ Sbjct: 67 DGRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMVG 126 Query: 121 LTPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQ 180 L R P +LSGGQQQR A+ARA+V ++L+DEPL+ LDYKLR ++R EL ++ + Sbjct: 127 LAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRRE 186 Query: 181 SGAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPL--N 238 G F++ T + EA + +N+G V Q G +EVY +PVN+ A + + Sbjct: 187 MGITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVGETNVFEG 246 Query: 239 TLDVTKSGNVFTRPSGVTIPVPSHLAVVPDGPVTIAFHPHHLGL---APQTGDAARLQAR 295 + G + G T + SH P + + P L + P+ D L R Sbjct: 247 VAGQSDGGILQALVEGRTCELSSHRGFQPGDRIRVLLRPEDLLVEREEPEDDDKLWLPGR 306 Query: 296 TLVSEITGS 304 + + GS Sbjct: 307 IMETVYKGS 315 Lambda K H 0.319 0.136 0.392 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: 302 Number of extensions: 11 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: 358 Length of database: 370 Length adjustment: 29 Effective length of query: 329 Effective length of database: 341 Effective search space: 112189 Effective search space used: 112189 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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