Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate H281DRAFT_02040 H281DRAFT_02040 putative spermidine/putrescine transport system ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__Burk376:H281DRAFT_02040 Length = 356 Score = 278 bits (712), Expect = 1e-79 Identities = 155/331 (46%), Positives = 213/331 (64%), Gaps = 8/331 (2%) Query: 18 VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77 +++ + K F + D+ I GEF+T LGPSGCGKTTVLR+IAG ET G I LD Sbjct: 4 LEIENLHKSFGTNIALHHFDMKIERGEFITFLGPSGCGKTTVLRMIAGFETPTRGVIRLD 63 Query: 78 NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQL 137 N+D+TH+ R V VFQSYALFP+MTV EN+ FGL++ P AEI+ RV E L +++L Sbjct: 64 NKDVTHLRTRQRKVGMVFQSYALFPNMTVAENIGFGLKITHRPQAEISQRVEEMLHLIKL 123 Query: 138 ETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKL 197 R P QLSGGQQQRVA+ARA+ KP++LLLDE LSALD K+R ++ +++ALQR+L Sbjct: 124 PQLGGRYPWQLSGGQQQRVALARALAGKPQVLLLDEPLSALDAKIRISLRQDIRALQREL 183 Query: 198 GITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNAT 257 GIT +FVTHDQEEAL++SDRIVVM +GR+EQ G+P EIY P+ FVA F+G +N+ Sbjct: 184 GITSIFVTHDQEEALSISDRIVVMNEGRVEQIGSPSEIYNYPRTRFVASFVGTLNILAGH 243 Query: 258 VIERLDEQRVRANVEGRECNIYVNF-AVEPGQKLHVLLRPEDLRVEEINDDNHAEGLIGY 316 VI+ + V V+G+E A + G+K + LRPE + +E + L Sbjct: 244 VIDPATGKMV---VDGQELTTTQELPAGDAGKKRLLALRPEAIVLEPAAPGRNT--LSAT 298 Query: 317 VRERNYKGMTLESVVELENGKMVMVSEFFNE 347 V E N+ G + +++ V+ + FN+ Sbjct: 299 VEEVNFLGAVVRIRTRVKDA--VISLDVFND 327 Lambda K H 0.319 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: 345 Number of extensions: 17 Number of successful extensions: 1 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: 378 Length of database: 356 Length adjustment: 30 Effective length of query: 348 Effective length of database: 326 Effective search space: 113448 Effective search space used: 113448 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 (21.7 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