Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate WP_069331237.1 C8J29_RS14155 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= reanno::Smeli:SM_b21216 (360 letters) >NCBI__GCF_003046325.1:WP_069331237.1 Length = 349 Score = 322 bits (825), Expect = 9e-93 Identities = 171/358 (47%), Positives = 236/358 (65%), Gaps = 10/358 (2%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M+ + +R++RK Y +E + G+D+ + GEF+V++G SGCGKSTLL ++AGL E + G+I Sbjct: 1 MAEISLRDVRKSYSGLEVIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEITAGEI 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 IG R V + P++RDIAMVFQ+YALYP+++V N+ +GL + ++ +AE ++ V +A++ Sbjct: 61 AIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAKLSKAEIEERVARSAKM 120 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 L++ LLDRKP QLSGGQRQRVA+GRALVRNP FL DEPLSNLDAKLR++MR ++K L Sbjct: 121 LELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRLQIKELQ 180 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240 + +RTT +YVTHDQ+EAMTLA R+ VM G EQ+A P E+YDRPAT +VAGF+GSP MN Sbjct: 181 RTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFIGSPAMN 240 Query: 241 ILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASV 300 +L A + L++ G +P P AGR + +GIRPE L AG E V Sbjct: 241 MLPARGLGDALEVAGQRLAVPAP--------AGRDLILGIRPEHLH-PAGPEEPGFELHV 291 Query: 301 EVVELTGPELVTTATVG-SQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPESGRSL 357 + VE G + ++ + P + V D ALHLFD +GR L Sbjct: 292 QAVEWLGADAFAHGSLADGTDLVLRTPGKAPVRERDRLKVAPDAAALHLFDAGTGRRL 349 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: 378 Number of extensions: 18 Number of successful extensions: 3 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: 349 Length adjustment: 29 Effective length of query: 331 Effective length of database: 320 Effective search space: 105920 Effective search space used: 105920 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 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