Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate 5207560 Shew_0094 ABC transporter-related protein (RefSeq)
Query= CharProtDB::CH_024626 (378 letters) >FitnessBrowser__PV4:5207560 Length = 369 Score = 164 bits (416), Expect = 3e-45 Identities = 94/249 (37%), Positives = 144/249 (57%), Gaps = 8/249 (3%) Query: 25 KCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIM------LDN 78 K F + + + GE L ++GPSG GK+T++R+IAGL +SG I + Sbjct: 11 KIFQQEGIALDAEFVCKAGEVLAVVGPSGGGKSTLMRMIAGLTKPESGEIRYGDSVWFSS 70 Query: 79 EDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLE 138 E ++ + R++ V Q + LFP+MT NV L P AE R + L V L Sbjct: 71 ESGRYLTPQQRHLGYVPQHFGLFPNMTALANVVAAL--DHIPKAERVARAKDWLERVNLH 128 Query: 139 TFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLG 198 R P LSGGQ+QRVA+ARA+ +PR+LLLDE SA+D + R+++ EL L+ +L Sbjct: 129 GLPDRLPANLSGGQRQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKEQLA 188 Query: 199 ITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNATV 258 I + VTHD EAL ++DR++++ G + Q G+PRE+ P+N VA +G N+F+A V Sbjct: 189 IPVIMVTHDLNEALLLADRMILISQGTLLQQGSPREVLSRPRNEAVAKQMGLRNLFDAHV 248 Query: 259 IERLDEQRV 267 + + E+++ Sbjct: 249 VAQEAERQI 257 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: 302 Number of extensions: 13 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: 378 Length of database: 369 Length adjustment: 30 Effective length of query: 348 Effective length of database: 339 Effective search space: 117972 Effective search space used: 117972 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: 50 (23.9 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