Align Sugar ABC transporter permease (characterized, see rationale)
to candidate PfGW456L13_146 Ferric iron ABC transporter, permease protein
Query= uniprot:A0A161ZE72 (280 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_146 Length = 521 Score = 57.8 bits (138), Expect = 5e-13 Identities = 64/218 (29%), Positives = 97/218 (44%), Gaps = 24/218 (11%) Query: 11 LRLGFWCLIGVLLLYAVFPFYYAIVTSLKPSSALFEVSYWIENPDFSNYAAVLNQASF-L 69 ++LG W + G L + AI+ S P L YW+ AV A+F + Sbjct: 274 VQLGPWAVAGQL-----YCLLLAIIGSGIPLGMLV---YWL---------AVGTSAAFPV 316 Query: 70 RAIGNSLV--VALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQVAVLSGL 127 AIG +L+ +AL + AL L L L V+++G+ L + ++ L Sbjct: 317 AAIGEALLSSLALSLGGAALCLVLAVPVGLLVVRYKGQLATWAERLPYLLHALPGLVIAL 376 Query: 128 FEVIRALG----LYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWV 183 V AL LY TS L+++Y + LP + T + + +LEEAA GAS + Sbjct: 377 TLVYFALHYVPMLYQTSALLLIAYALLFLPLAQAPIRTALNKAAPQLEEAARTLGASSFS 436 Query: 184 TLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLT 221 RV LP+++PAL L F+ A E L + T Sbjct: 437 AFCRVTLPIIFPALGAAFALVFLDAMKELTATLLLSPT 474 Score = 45.1 bits (105), Expect = 3e-09 Identities = 39/142 (27%), Positives = 57/142 (40%), Gaps = 9/142 (6%) Query: 74 NSLVVALCVVTLALFLSLTAAYALGRVKFRGR---GTVLMMVLGVSMFPQVAVLSGLFEV 130 N+L + + V + + L+ A+ L R GR G +L + V F L Sbjct: 70 NTLALMIGVTIVCGVIGLSLAWLLERSNLPGRRLWGVILCLPFAVPAFVSSFTWVSLSAH 129 Query: 131 IRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLL 190 LG IL ++ P + + L LEE+A G + W RV L Sbjct: 130 FEGLG------GAILVMSLSKYPLIFLPVAATLRNLDPSLEESARTLGQNRWGVFFRVTL 183 Query: 191 PLLWPALVTTGLLAFIAAWNEF 212 PLLWP+L+ LL + EF Sbjct: 184 PLLWPSLLAGSLLIALHMLVEF 205 Lambda K H 0.329 0.141 0.433 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: 385 Number of extensions: 21 Number of successful extensions: 2 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: 280 Length of database: 521 Length adjustment: 30 Effective length of query: 250 Effective length of database: 491 Effective search space: 122750 Effective search space used: 122750 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 (21.8 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