Align ABC transporter for Lactose, ATPase component (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 208 bits (529), Expect = 2e-58 Identities = 131/364 (35%), Positives = 195/364 (53%), Gaps = 35/364 (9%) Query: 4 LQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTID 63 +++ ++ K +G + V L I +GE V +GPSGCGK+TLLR+IAG+E G + + Sbjct: 3 IEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFE 62 Query: 64 DVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPR------AEIEKRVNEA 117 + +R + VFQ YAL+ HM V EN+ F LR PR +EI KRV + Sbjct: 63 GSEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVK--PRKERPCESEIRKRVMDL 120 Query: 118 AHILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIA 177 +++L L DR P QLSGGQRQR+A+ RA+ PK+ L DEP LD ++R +R + Sbjct: 121 LSLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLR 180 Query: 178 RLHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSP 237 RLH ++ + V+VTHDQ EA+ +AD++VVM G +EQVGSP ++Y +PA+ FV F+G+ Sbjct: 181 RLHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGN- 239 Query: 238 KMNFLKGVIEIDEDQAYARLPDYGDAKIPVTLQAAAGTAVTIGIRPEHFD---EAGPAAL 294 + + + + + +P AG IRP D A P +L Sbjct: 240 --------VNVFHSRVHGAWAEVARDDVP------AGQEAVAFIRPHDIDIDTVATPESL 285 Query: 295 DLAIDMLEHLGGETFAYARHHGNGELIVVETKNGR----GLKTGDRLTARFDPVSVLVF- 349 + + ++ +G H GEL+ VE R GL G ++ + P V VF Sbjct: 286 EAKVSYVQTIGPLVRVEVIH--QGELVEVELTRERQQVLGLTAGQQVWLK--PRQVKVFA 341 Query: 350 DGEG 353 +GEG Sbjct: 342 NGEG 345 Lambda K H 0.321 0.139 0.396 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: 325 Number of extensions: 13 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: 358 Length of database: 360 Length adjustment: 29 Effective length of query: 329 Effective length of database: 331 Effective search space: 108899 Effective search space used: 108899 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