Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= reanno::Smeli:SM_b21216 (360 letters) >NCBI__GCF_900167125.1:WP_078717009.1 Length = 370 Score = 217 bits (552), Expect = 5e-61 Identities = 115/285 (40%), Positives = 175/285 (61%), Gaps = 3/285 (1%) Query: 2 SALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDIL 61 S + + ++ K + L + + + GEFL +LG SGCGK+TLL ++AG PS G+I+ Sbjct: 6 SVIRLEHVAKEFDGETVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEII 65 Query: 62 IGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLL 121 + RS+ V P R + VFQSYAL+P++SV N+ FGL M +P+ E + V R++ Sbjct: 66 LDGRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMV 125 Query: 122 QIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQ 181 + R+P+ LSGGQ+QRVAI RA+V P V L DEPLS LD KLR++MRTELK+L + Sbjct: 126 GLAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRR 185 Query: 182 MLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNI 241 + T ++VTHDQ EA +++ R+ VM +G + Q+ P EVY++P ++VA FVG N+ Sbjct: 186 EMGITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVGE--TNV 243 Query: 242 LDAEM-TANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEAL 285 + ++G ++ E + + G R++V +RPE L Sbjct: 244 FEGVAGQSDGGILQALVEGRTCELSSHRGFQPGDRIRVLLRPEDL 288 Lambda K H 0.320 0.136 0.385 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: 321 Number of extensions: 14 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: 360 Length of database: 370 Length adjustment: 30 Effective length of query: 330 Effective length of database: 340 Effective search space: 112200 Effective search space used: 112200 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: 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