Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate H281DRAFT_04922 H281DRAFT_04922 iron complex transport system permease protein
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__Burk376:H281DRAFT_04922 Length = 663 Score = 152 bits (383), Expect = 3e-41 Identities = 106/327 (32%), Positives = 167/327 (51%), Gaps = 16/327 (4%) Query: 11 WGLPVAALIIIFWLSLFCYSA-IPVSGADATRALLPGHTPTLPEALVQNLRLPRSLVAVL 69 W LP L++ WL SA +PV A +L G TL + +V+ LPR +A++ Sbjct: 16 WRLPALLLMLAAWLVYHTLSARLPV--AQWPGVVLSGADATLQQLVVRYGWLPRVAIALI 73 Query: 70 IGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSLSFIAACGG 129 GA+L+LAG + Q + NP+A P LG+++GA LA+ + + ++P +A + +A G Sbjct: 74 AGAALSLAGVVFQQVLRNPLAEPLTLGVSAGAYLALTIAAVVAPALVADMRFT-VALTGA 132 Query: 130 GVSWL--LVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYGIFYWLAG 187 ++ L + MT GF ++LAG+ ++ +C L+ + ++ E +F W G Sbjct: 133 ALAMLATMAMTWRKGFAAV----SIVLAGMIVNLYCGALSVLLTIVFERSLTSVFIWGGG 188 Query: 188 GVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVL 247 + W V LLP V+ LL L L +L D +A LG++L R V + + Sbjct: 189 SLVQNGWAGVVWLLPRVLACGAAAALLVRPLTLFSLDDGSASQLGMSLAWTRPVALAIAV 248 Query: 248 LLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFP 307 +L S G + FIGL P LAR R+ L + L+GA L+ +AD ++L P Sbjct: 249 ILSAFVASAVGVIGFIGLGGPVLARLMGARRLRDQLLWAPLVGALLLAIADQAVQSL--P 306 Query: 308 GD----LPAGAVLALIGSPCFVWLVRR 330 G LP GA +AL G P +W++RR Sbjct: 307 GVLGELLPTGAAVALCGGPLLLWMLRR 333 Score = 150 bits (380), Expect = 7e-41 Identities = 120/339 (35%), Positives = 174/339 (51%), Gaps = 38/339 (11%) Query: 3 AIKHPVLLWG-LPVAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRL 61 A++ PVLL G L VAA++I C+S + + G T A H V R+ Sbjct: 352 ALRVPVLLLGGLLVAAVVISL-----CFS-VTMQGWQWTDAQ---HWSD-----VWFWRV 397 Query: 62 PRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSL 121 PR ++ G +ALAGT+LQ +T NPMASP LLG++ GA L M + + ++ P L Sbjct: 398 PRLTASLGAGVMVALAGTILQRVTGNPMASPDLLGVSGGAMLGMLVAAVVATEPSTPVLL 457 Query: 122 SFIAACGGGVSWLLVMTAG--GGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAY 179 + AA G V L ++T G GF H ++LAGIA+SAF + I L A AY Sbjct: 458 AGSAA-GALVCLLTIVTLGRRSGFAPEH----VLLAGIAISAFAQAV--IMLATASGGAY 510 Query: 180 GIFYWLAGGVSHARWQDVWQLLPVV--------VTAVPVVLLLANQLNLLNLSDSTAHTL 231 A + ++ + ++P V AV V L A L +L L + A L Sbjct: 511 ------ANLLRPLQYGSTYLIVPATAIAVGVCTVAAVLVAYLGARWLEILPLGANVADAL 564 Query: 232 GVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGA 291 GV R RL++ + +L V GP++F+GL+ PHLAR R+ + V+ L+G Sbjct: 565 GVGAQRARLLLLAVAAILTAGATVVIGPMSFVGLMAPHLARLLGFPRARSQMLVAALIGG 624 Query: 292 TLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVRR 330 LM+L+D L R + FP +PAG + L+G P +WL+RR Sbjct: 625 LLMVLSDWLGRNMIFPQQMPAGVIATLLGGPYLMWLLRR 663 Lambda K H 0.327 0.140 0.436 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: 671 Number of extensions: 44 Number of successful extensions: 7 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: 332 Length of database: 663 Length adjustment: 33 Effective length of query: 299 Effective length of database: 630 Effective search space: 188370 Effective search space used: 188370 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 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