Align Fe(3+) dicitrate-binding periplasmic protein; Iron(III) dicitrate-binding periplasmic protein (characterized)
to candidate BWI76_RS11380 BWI76_RS11380 iron-dicitrate transporter substrate-binding subunit
Query= SwissProt::P15028 (300 letters) >FitnessBrowser__Koxy:BWI76_RS11380 Length = 300 Score = 416 bits (1069), Expect = e-121 Identities = 210/298 (70%), Positives = 244/298 (81%) Query: 1 MLAFIRFLFAGLLLVISHAFAATVQDEHGTFTLEKTPQRIVVLELSFADALAAVDVIPIG 60 M + +R LL + FA TVQDEHG FTL+KTPQRIVVLELSF DALAAV+V PIG Sbjct: 1 MFSLVRLCIFSLLFLAGPVFAVTVQDEHGRFTLDKTPQRIVVLELSFVDALAAVNVSPIG 60 Query: 61 IADDNDAKRILPEVRAHLKPWQSVGTRAQPSLEAIAALKPDLIIADSSRHAGVYIALQQI 120 +ADDND RIL +VRA LKPWQSVGTRAQPSLEAI+AL PDLI+ADSSRHAG+Y AL+QI Sbjct: 61 VADDNDPSRILSDVRACLKPWQSVGTRAQPSLEAISALHPDLIVADSSRHAGIYAALRQI 120 Query: 121 APVLLLKSRNETYAENLQSAAIIGEMVGKKREMQARLEQHKERMAQWASQLPKGTRVAFG 180 APVLLLKSRNET+ ENLQSAAIIG++VG+ EMQ RL QH+++MA ++ QLP G V FG Sbjct: 121 APVLLLKSRNETWEENLQSAAIIGKVVGQDEEMQRRLAQHRQKMAAFSRQLPAGASVLFG 180 Query: 181 TSREQQFNLHTQETWTGSVLASLGLNVPAAMAGASMPSIGLEQLLAVNPAWLLVAHYREE 240 TSREQQFNLH+ +T+TGSVLA+LGL VP GA M +I LEQLLA+NP WLLVAHYR E Sbjct: 181 TSREQQFNLHSSQTYTGSVLAALGLKVPLPNGGAPMAAINLEQLLALNPQWLLVAHYRAE 240 Query: 241 SIVKRWQQDPLWQMLTAAQKQQVASVDSNTWARMRGIFAAERIAADTVKIFHHQPLTV 298 SIV +WQQD LW +L A QKQQVA+VDS++WARMRGI AAERIA+D VKI HHQ + + Sbjct: 241 SIVTKWQQDALWPILQAEQKQQVAAVDSDSWARMRGIVAAERIASDMVKIVHHQAVDI 298 Lambda K H 0.320 0.131 0.381 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: 340 Number of extensions: 7 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: 300 Length of database: 300 Length adjustment: 27 Effective length of query: 273 Effective length of database: 273 Effective search space: 74529 Effective search space used: 74529 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 (21.9 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