Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate 3608624 Dshi_2017 ABC transporter related (RefSeq)
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Dino:3608624 Length = 333 Score = 285 bits (729), Expect = 1e-81 Identities = 157/309 (50%), Positives = 203/309 (65%), Gaps = 25/309 (8%) Query: 1 MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60 M+ L + N++K +G+ + + G+ I + GEF+V++G SGCGKSTLL ++AGL S G++ Sbjct: 1 MATLTLDNVKKSFGKTDVIHGVSIDVTEGEFIVIVGPSGCGKSTLLRMVAGLETVSSGEV 60 Query: 61 LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120 I R V + P DRDIAMVFQ+YALYP++SV N+ +GL++ +VP+AE V A+L Sbjct: 61 RIDGRVVNTLEPMDRDIAMVFQNYALYPHMSVFDNMAYGLKIAKVPKAEIADRVAVAAKL 120 Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180 LQ+E L RKP +LSGGQRQRVA+GRA+VR P VFLFDEPLSNLDAKLR++MR E+K L Sbjct: 121 LQLEPYLGRKPKELSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEIKALQ 180 Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240 + L T +YVTHDQ+EAMTLA R+ VM G +Q+ AP EVY P T +VAGF+GSPP N Sbjct: 181 RELGVTSLYVTHDQVEAMTLADRMIVMNGGVADQIGAPLEVYANPQTAFVAGFIGSPPTN 240 Query: 241 ILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTASV 300 L A+M G PA +VGIRPE LR+A RL A V Sbjct: 241 FLPADMVRAG------------PAG----------QQVGIRPEHLRVAPQG---RLEAHV 275 Query: 301 EVVELTGPE 309 E G E Sbjct: 276 AYAEALGAE 284 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: 315 Number of extensions: 9 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: 360 Length of database: 333 Length adjustment: 29 Effective length of query: 331 Effective length of database: 304 Effective search space: 100624 Effective search space used: 100624 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