Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate AZOBR_RS17950 AZOBR_RS17950 iron ABC transporter
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__azobra:AZOBR_RS17950 Length = 658 Score = 166 bits (420), Expect = 2e-45 Identities = 104/272 (38%), Positives = 148/272 (54%), Gaps = 5/272 (1%) Query: 60 RLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGY 119 R PR VA GA LA AG LLQ +T NP+ASP +LG+ +GA + LT+AL G+ Sbjct: 385 RGPRVAVAAAAGAMLAAAGMLLQRVTANPLASPEILGVGTGAGVG--LTAALFLVAAPGF 442 Query: 120 SLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAY 179 + A+ G V L M A R +L+LAGIA+SA C + + A+ Sbjct: 443 GVQLAASAAGAVLTLAAMLALS-LRAGFGPERLLLAGIAMSALCSAVLTAVIATGTPQAF 501 Query: 180 GIFYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLR 239 + WL+G + A D W + V V + + L A L +L L D TA +G+ + R R Sbjct: 502 ALLRWLSGSTNEAGPGDAWFCIGVAVLLLATLPLTAKWLEILPLGDVTAQAVGLPVRRCR 561 Query: 240 LVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPV-SMLLGATLMLLAD 298 +++ +L LL A GP++FIGL+ PHLAR AG + + ++L+GA LM+++D Sbjct: 562 VLLVLLAGLLTAAAALFVGPLSFIGLIAPHLARL-AGLGRPLQQGIGAVLIGAGLMVVSD 620 Query: 299 VLARALAFPGDLPAGAVLALIGSPCFVWLVRR 330 LAR +AFP LP G AL+ P VWL+ R Sbjct: 621 WLARTVAFPYQLPLGLFAALLAGPYLVWLLGR 652 Score = 134 bits (337), Expect = 6e-36 Identities = 100/329 (30%), Positives = 163/329 (49%), Gaps = 20/329 (6%) Query: 8 VLLW-GLPVAALIIIFWLSLFCYSAIPVSGADATRAL-LPGHTPTLPEALVQNLRLPRSL 65 +LLW GL +AA + W V+G A ++ LP L ++ + LPR Sbjct: 6 ILLWSGLALAAAALSAW---------QVAGHAAAPSMPLPPDAAWLDGVILYHSVLPRIA 56 Query: 66 VAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYSLSFIA 125 VA++ GA+L L+G LLQ + NP+A PS LG+++GA LA+ L +P + ++ +A Sbjct: 57 VALVAGAALGLSGLLLQRVLRNPLAEPSTLGVSAGAQLALTLGMLYAPA-LMDHAREGVA 115 Query: 126 ACGG--GVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYGIFY 183 GG V +L MT +R + ++LAG+ ++ + +L ++ + IF Sbjct: 116 LAGGLAAVGLILAMT----WRRGLEPVAVVLAGMMVALTATMGSAALILANGEYLFSIFL 171 Query: 184 WLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVIN 243 W G ++ W + ++ V +LL L +L L D++A +LGV L R + Sbjct: 172 WGGGALAQQSWGPTLTIAVRLLIGVGAAVLLMRPLAILGLDDASARSLGVALNATRFGVI 231 Query: 244 MLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARA 303 + + L + + G + F+GL P LA Q L + L+GA L+ L D L + Sbjct: 232 GVAVWLAASVTAEVGVIGFVGLAAPALAHLSGARTQGQRLVAAPLIGALLLWLTDGLVQL 291 Query: 304 LA-FPGD-LPAGAVLALIGSPCFVWLVRR 330 LA G+ +P GA AL+G P +WL+ R Sbjct: 292 LAGVDGERVPTGAATALLGGPLLLWLLPR 320 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: 692 Number of extensions: 40 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: 658 Length adjustment: 33 Effective length of query: 299 Effective length of database: 625 Effective search space: 186875 Effective search space used: 186875 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