Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_000744815.1:WP_037573817.1 Length = 369 Score = 306 bits (785), Expect = 4e-88 Identities = 178/351 (50%), Positives = 228/351 (64%), Gaps = 12/351 (3%) Query: 14 GAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGERVNDVPPS 73 G + +DL+I +GEF+V VGPSGCGKST LRM+AGLE++ G + I V +PP Sbjct: 16 GDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNGAIRIGERDVTHLPPK 75 Query: 74 KRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTPYLDRLPKA 133 R IAMVFQ+YALYPHMTV DNM F ++IA +K EI +V AA +L LT +LDR PKA Sbjct: 76 DRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAAKILDLTEFLDRKPKA 135 Query: 134 LSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSDTTMIYVTH 193 LSGGQRQRVA+GRAI R P+VFL DEPLSNLDA LRV+TR +IA L R+ TT +YVTH Sbjct: 136 LSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAGLQRRLGITT-VYVTH 194 Query: 194 DQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPATITATGQQ 253 DQVEAMT+ DR+ VL G ++QV P +Y+RPANLFVA FIGSPAMN++ IT G + Sbjct: 195 DQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPAMNLVEVPITDGGVK 254 Query: 254 TAVSLAGGKSVTLDVPTNASENG-KTASFGVRPEDLRV---TE--ADDFLFEGTVSIVEA 307 S+ V+ D A+ G KT + GVRPE L + TE +D TV++VE Sbjct: 255 FGESVV---QVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEGGGEDKGLAVTVNVVEE 311 Query: 308 LGEVTLLYIEGLVENEPI--IAKMPGIARVGRGDKVRFTADKAKLHLFDTN 356 LG +Y V E I + ++ G +GD++R + H+F T+ Sbjct: 312 LGADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRAGETHVFSTS 362 Lambda K H 0.320 0.137 0.387 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: 414 Number of extensions: 16 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: 362 Length of database: 369 Length adjustment: 30 Effective length of query: 332 Effective length of database: 339 Effective search space: 112548 Effective search space used: 112548 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