Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate RR42_RS18590 RR42_RS18590 hypothetical protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Cup4G11:RR42_RS18590 Length = 359 Score = 318 bits (814), Expect = 2e-91 Identities = 177/361 (49%), Positives = 236/361 (65%), Gaps = 6/361 (1%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M++++IR I+K +G + ++G+DI + G+F VL+G SGCGKSTLL +IAGL E + G+I Sbjct: 1 MASVQIRGIQKYFGSTQVIRGVDIDIADGQFTVLVGPSGCGKSTLLRMIAGLEEITTGEI 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 IG R V + PK+RDIAMVFQ+YALYP+++V N+ F L++ + + E + V + + Sbjct: 61 AIGNRVVNRLPPKERDIAMVFQNYALYPHMTVYDNMAFSLKLAKGDKEEIKRKVAKASAI 120 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 L +++LL+R P QLSGGQRQRVA+GRA+VR+PQVFLFDEPLSNLDAKLR++MR E+K LH Sbjct: 121 LGLDSLLERYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKELH 180 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240 Q LRTT VYVTHDQIEAMT+A +I VMRDGR+EQ P +YD P L+VAGF+GSP MN Sbjct: 181 QRLRTTSVYVTHDQIEAMTMADQIVVMRDGRVEQRGKPLALYDHPDNLFVAGFIGSPAMN 240 Query: 241 ILDAEMTANG--LKIEGCEEV-LPLPAAFNGAAWA-GRRVKVGIRPEALRLAAGSEAQRL 296 + + +G +E + LP PA F+ A G+RV G+RPE L L G Q L Sbjct: 241 FVPGVLRRSGGDAAVEFPDGTRLPAPARFDATAGTDGQRVIYGVRPEHLTL--GMPGQGL 298 Query: 297 TASVEVVELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPESGRS 356 V VVE TG + + R G D HLFD +SG++ Sbjct: 299 QTRVSVVEPTGANTEIYSRFCEAEFISIFRERHDFAAGDILNLVPDHQHTHLFDADSGQT 358 Query: 357 L 357 L Sbjct: 359 L 359 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: 365 Number of extensions: 15 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: 359 Length adjustment: 29 Effective length of query: 331 Effective length of database: 330 Effective search space: 109230 Effective search space used: 109230 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 17 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