Align Putrescine transport system permease protein PotI (characterized)
to candidate BPHYT_RS23135 BPHYT_RS23135 putrescine/spermidine ABC transporter permease
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__BFirm:BPHYT_RS23135 Length = 303 Score = 318 bits (814), Expect = 1e-91 Identities = 153/266 (57%), Positives = 205/266 (77%), Gaps = 4/266 (1%) Query: 15 ILLLGFTFLYAPMLMLVIYSFNSSKLVTVWAGWSTRWYGELLRDDAMMSAVGLSLTIAAC 74 +L GF FLY P++ L++YSFN SKLVTVW+G+S +WYG LL+D +++A LSL I Sbjct: 12 VLTFGFLFLYIPIISLIVYSFNESKLVTVWSGFSLKWYGALLQDGELLNAAWLSLKIGLL 71 Query: 75 AATAAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVALAHAIGW 134 A A+ ++GT A VL RFGRFRG FA MI APLV+P+VI G+SLLLLFVAL +GW Sbjct: 72 TACASVVIGTWAGFVLARFGRFRGFTLFAGMINAPLVIPEVIQGISLLLLFVALEQMLGW 131 Query: 135 PADRGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVITLPMIM 194 P RG+ TIW+ HV C +YVA+++ SR++EL+RS+EEAA+DLGATP KVFF+ITLP+I Sbjct: 132 PKGRGLFTIWIGHVMLCVSYVAIIVQSRVKELNRSLEEAALDLGATPFKVFFLITLPLIS 191 Query: 195 PAIISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALATLILGAV- 253 A++SGWLL+FTLS DDLV+++F+SGPG+TTLP++VFS VR+G+NPE+NALAT+ + V Sbjct: 192 QALMSGWLLSFTLSFDDLVLSAFLSGPGSTTLPLVVFSRVRLGLNPEMNALATIFITTVT 251 Query: 254 -GIVGFIAWYLMARAEKQRIRDIQRA 278 G++ W M E++R RD+Q A Sbjct: 252 IGVIAVNRW--MQLRERKRNRDMQMA 275 Lambda K H 0.330 0.140 0.430 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: 304 Number of extensions: 15 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: 281 Length of database: 303 Length adjustment: 26 Effective length of query: 255 Effective length of database: 277 Effective search space: 70635 Effective search space used: 70635 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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