Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate RR42_RS07435 RR42_RS07435 (Fe-S)-binding protein
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__Cup4G11:RR42_RS07435 Length = 469 Score = 305 bits (780), Expect = 4e-87 Identities = 171/465 (36%), Positives = 263/465 (56%), Gaps = 7/465 (1%) Query: 9 EYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADAKDHAAKNMDTL 68 E++ + L ++ L+ + K + + +RA+A +DID A + + +D A +N+D Sbjct: 7 EFKARAGQKLADQRLQQNLKKLSTKFVTARADAIRDIDFDATREALKERRDRALQNLDVW 66 Query: 69 YAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLEED 128 A F+ A +RG V A T A+A ++A IA+ + KK IKSKSM EE LN L E Sbjct: 67 LATFEENATRRGATVLFAETTADAARLVAEIAQKHGVKKVIKSKSMVTEEMRLNQVLGEM 126 Query: 129 NVEVIETDLGEWIIQMRH-EGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDIQRLVKVA 187 V+ IETDLGE+I+Q+ E PSH++ P +H + ++ADLF++V + + DI + + A Sbjct: 127 GVQSIETDLGEYILQINDAEPPSHIIAPVVHKDKEEIADLFAKVHHKPRLTDISEMTREA 186 Query: 188 RRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPTL 247 R LR F +ADMG++G NF +AETG++ +VTNEGN + T +PRVHVA+ G++K++PTL Sbjct: 187 REVLRPEFLSADMGVTGGNFIIAETGSVAVVTNEGNEGMCTVMPRVHVAVTGIEKVLPTL 246 Query: 248 HDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALAEDPLF 307 D +++LPR+ATGQAI++Y + + G E DG + M+ V +D GR L F Sbjct: 247 EDLATVMRLLPRSATGQAISNYFSLLTGP-RAEGERDGPEHMYFVLVDGGRSGLIGGD-F 304 Query: 308 SQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINCE 367 +LRC+RCGAC N CPVY+ +GGH G +Y G +G +LT + G A +L Q C Sbjct: 305 QDMLRCIRCGACMNHCPVYQKIGGHAYGWVYPGPMGSVLTPSYVGIANALDLPQAATLCG 364 Query: 368 SCKHICAGGIDLPRLIKEIRARLNEEEGMPVETTL----MGKMLKNRKLFHTLLRFAKWA 423 C +C I L L++++R + E P + L G + + L+ R Sbjct: 365 ECNRVCPASIPLSDLLRKLREKQMERGLRPWQERLGLQVWGFVARRPGLYAFATRIGARL 424 Query: 424 QKPVTGGTPYIRHLPQIFAKDHGFKALPAIADKPFRDEWETVRPR 468 + G + I LP + LPA + + FR+ ++ R R Sbjct: 425 LARMGGSSKLIARLPMAGRGWTETRDLPAPSGRTFRELYKERRAR 469 Lambda K H 0.321 0.135 0.402 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: 730 Number of extensions: 39 Number of successful extensions: 4 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: 717 Length of database: 469 Length adjustment: 36 Effective length of query: 681 Effective length of database: 433 Effective search space: 294873 Effective search space used: 294873 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: 53 (25.0 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