Align ABC transporter permease (characterized, see rationale)
to candidate WP_013093544.1 BC1002_RS29030 ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000092885.1:WP_013093544.1 Length = 607 Score = 209 bits (531), Expect = 2e-58 Identities = 112/292 (38%), Positives = 167/292 (57%), Gaps = 17/292 (5%) Query: 9 INGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGAPGWV 68 INGL++G++YAL+A+G +++G+ LINFAHG V M+G W C+ + +P Sbjct: 9 INGLIVGNIYALLAVGLALIFGVSHLINFAHGSVYMVGGFIGWLCLTRLGLPLP------ 62 Query: 69 ILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWKPNYK 128 + LLAT+ C A L +IE++ RPL+ + R+APL+ IG+S +L LA I++ P+ + Sbjct: 63 VALLATVAGC---ALLGILIERIGLRPLQGAARIAPLLATIGISFVLDQLAQIVFGPDPR 119 Query: 129 PYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAENPRVAS 188 P P+ LP IGGA I +LI + A L + T LG A+RATA++ A Sbjct: 120 PVPSSLPDWTLSIGGATIGSLDLLIAAIGIGAAGVLYLFLRFTRLGWAVRATAQDRDAAQ 179 Query: 189 LMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGGIGNLA 248 MGV + V A F I L ++G++ Y + MGF LK A + GG+GN+ Sbjct: 180 QMGVNVNAVNQAVFAIACGLGGLSGLLVGMYYNSIDPAMGFQATLKGVVALLIGGLGNVP 239 Query: 249 GAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 GA+ G +LLGL+E+ G L G+ Y D+FAF++L+ L RP+GL Sbjct: 240 GAIAGSLLLGLVESYGV--------ALFGTSYRDLFAFVLLLAFLVWRPNGL 283 Score = 72.8 bits (177), Expect = 2e-17 Identities = 75/299 (25%), Positives = 129/299 (43%), Gaps = 29/299 (9%) Query: 8 IINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGAPGW 67 ++ L G +Y L+AL T+V G + I+ H +L+IGA S + + + G P Sbjct: 332 VLQTLTNGWIYGLLALSLTLVAGTVGQISLGHAALLLIGAYAS-ALLSVNLGWSPA---- 386 Query: 68 VILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWKPNY 127 L +A ++ A + V+ ++R +A L IG I L ++ W Sbjct: 387 ----LTIPLAGLITAAIGTVLIYPSFRLRGHYVSIATL--GIGEII---GLVVLNWDSLT 437 Query: 128 KPYPTMLPSSPFEIGGAFITPTQILILGVTAVA--LASLVYLVNHTNLGRAMRATAENPR 185 + + P + G +T + + AV LA L + H++LGR RA E+ Sbjct: 438 RGPVGITGIVPLSLFGWQLTGVRAVYWFTLAVLVLLALLQARLLHSHLGRTWRAIREDDV 497 Query: 186 VASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQH-TMGFLPGLKAFTAAVFGGI 244 A G++P+ + F G + A I G + A Y + T + A T + GG+ Sbjct: 498 AARAYGIRPNRYKAIAFACGGLAAGIGGGIAAHLYSYINYQTFDSQVSILALTMVILGGL 557 Query: 245 GNLAGAVVGGI-LLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLLG 302 G++ GAV G + L+ L E + Y + ++L++++ RP GL G Sbjct: 558 GSVIGAVAGAVALISLPELF-----------RFAADYRMLIYGMILLLLVRFRPQGLFG 605 Lambda K H 0.327 0.142 0.419 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: 453 Number of extensions: 30 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 309 Length of database: 607 Length adjustment: 32 Effective length of query: 277 Effective length of database: 575 Effective search space: 159275 Effective search space used: 159275 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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