Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate BPHYT_RS20235 BPHYT_RS20235 iron ABC transporter
Query= SwissProt::P15030 (332 letters) >FitnessBrowser__BFirm:BPHYT_RS20235 Length = 702 Score = 160 bits (405), Expect = 9e-44 Identities = 109/320 (34%), Positives = 167/320 (52%), Gaps = 7/320 (2%) Query: 11 WGLPVAALIIIFWLSLFCYSAIPVSGADATRALLP-GHTPTLPEALVQNLRLPRSLVAVL 69 W L +AL+++ + + ++ + A R L H L L+ +LRLPR + A+L Sbjct: 376 WPLTASALVLLGVVLVCAGASFGPTTIGAQRWLAAFDHRDELARMLL-DLRLPRLICALL 434 Query: 70 IGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAGYS-LSFIAACG 128 GA LA +G L+Q++ NP+A P +LG+ GA LA +AL P+A +S L+ + G Sbjct: 435 AGALLAASGVLMQSIVRNPLAGPEVLGVTQGAGLATL--AALVMWPLANHSTLAAASLAG 492 Query: 129 GGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHAYGIFYWLAGG 188 GG++ L + RH + + L GI + L++ + WL GG Sbjct: 493 GGITLALTLLLNR--RHRYAPLAVALTGIVIGTLWTTLSQWLITQQSVQPARFVVWLVGG 550 Query: 189 VSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLL 248 W +V LLP V A+PV LLA L+LL L D A +LG+ + LR ++ + L Sbjct: 551 TYGRSWGEVTTLLPWCVLALPVFALLARPLDLLALGDDQAASLGLPIGVLRPLVLTVATL 610 Query: 249 LVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPG 308 A V+ GPV FIGL+ PHLA R L ++ GA ++++AD+ AR L P Sbjct: 611 AACAAVAAVGPVGFIGLMAPHLASMLGARAHRTRLWLAAACGALVLVVADIAARTLLAPR 670 Query: 309 DLPAGAVLALIGSPCFVWLV 328 ++PAG + ALIG+P + L+ Sbjct: 671 EIPAGVLTALIGAPYLLALL 690 Score = 142 bits (359), Expect = 2e-38 Identities = 110/339 (32%), Positives = 168/339 (49%), Gaps = 32/339 (9%) Query: 4 IKHPVLLWGLPVAALIIIFWLSLFC-----YSAIPVSGADATRALLPGHTPTLPEALVQN 58 +K V G + ALI+I + + A P +G+DA + L L+ + Sbjct: 24 VKSRVTTIGAALVALIVIVAVMRLAPGFRTWLAAP-TGSDAAQ---------LAGILLFD 73 Query: 59 LRLPRSLVAVLIGASLALAGTLLQTLTHNPMASPSLLGINSGAALAMALTSALSPTPIAG 118 L +PR L A++ G LA+AGTL Q+LT NP+ASP LLGI GA L + L + L P+ Sbjct: 74 LSVPRILAALVAGGCLAVAGTLFQSLTRNPLASPDLLGITGGAQLGL-LAAMLVPSLAGV 132 Query: 119 YSLSFIAACGGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAEDHA 178 S+ + ACG G + V A GG+R T R L+LAG LT + L E Sbjct: 133 ASVPLLFACGLGAA-ACVAAAAGGWRATPLR--LVLAGSVCMLLFSALTTLILAFFEQSI 189 Query: 179 YGIFYWLAG-----GVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGV 233 G+ W +G G + + W +LP++ A+P V+ L+ L L D A GV Sbjct: 190 VGVSLWASGSLYQPGAAGLKIAASWLVLPLI--ALPFVI---RPLDPLALGDDAAAAAGV 244 Query: 234 NLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRN---VLPVSMLLG 290 + RL ++ + VSVAGP++++GL+ P+L R G ++P+S L+G Sbjct: 245 RVDATRLAAMVVAVGFASVAVSVAGPLSYVGLIAPNLLRQMRGAKASRLAALVPLSALVG 304 Query: 291 ATLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWLVR 329 L+L+ D +AL L G +A +G+P + ++R Sbjct: 305 GALVLVTDSAVQALDLDATLSTGVAIAFVGTPLMLAMIR 343 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: 663 Number of extensions: 41 Number of successful extensions: 8 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: 702 Length adjustment: 34 Effective length of query: 298 Effective length of database: 668 Effective search space: 199064 Effective search space used: 199064 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