Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate CA265_RS18400 CA265_RS18400 iron-sulfur cluster-binding protein
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__Pedo557:CA265_RS18400 Length = 461 Score = 270 bits (691), Expect = 9e-77 Identities = 156/422 (36%), Positives = 230/422 (54%), Gaps = 19/422 (4%) Query: 53 EVADAKDHAAK-----NMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKK 107 E + K H K N+D +F++ ++RG KV A A EA + I I + NN K Sbjct: 46 EASKKKAHVIKWRVMENLDKFLPEFESNFQRRGGKVIWANDAEEAQQEILNIIKRNNGKT 105 Query: 108 AIKSKSMTAEETHLNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADL 167 IKSKSMT EE HLN LE++N+E +E+DLGE+I+Q+ + P H+V PA+HLS +A L Sbjct: 106 VIKSKSMTTEEIHLNDFLEKNNIESLESDLGEYIVQLLGQAPYHIVTPAMHLSATDIAQL 165 Query: 168 FSEVTKQKQEVDIQRLVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLV 227 F + + +LV+ AR LR + AD+GISG NF +A+TG+I L NEGNARL Sbjct: 166 FHDKFGTPIDATPPQLVQKARELLRDKYLNADIGISGGNFLIADTGSIALTENEGNARLS 225 Query: 228 TTLPRVHVALAGLDKLVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRK 287 TT P++H+A+ G++K++P++ D +L + TGQ +T Y T + G + DG + Sbjct: 226 TTFPKIHIAIVGIEKVIPSIADLDLFWPLLASHGTGQNLTVYNTILSGPRQPNE-TDGPE 284 Query: 288 EMHIVFLDNGRRALAEDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILT 347 EM+++ LDNGR L Q L C+RCGAC N CPVY+ +GGH Y G IG ++T Sbjct: 285 EMYVILLDNGRTNLLAQKDQRQGLYCIRCGACLNACPVYKNIGGHTYNTTYSGPIGSVIT 344 Query: 348 YFFHGRDKARNLVQNCINCESCKHICAGGIDLPR--LIKEIRARLNEEEGMPVETTLMGK 405 G ++ ++L C C +C ID+ + L+ A E G E Sbjct: 345 PHLKGMEEFKHLSYASSLCGKCSEVCPVKIDIHKMLLLNRRDAAAGHENGKKEEI----- 399 Query: 406 MLKNRKLFHTLLRFAKWAQKPVTGGTPYIRHLPQIFAKDHG-FKALPAIADKPFRDEWET 464 +F +++ KW GG L + F K G ++ +P +ADK F +WE Sbjct: 400 ---GWSMFSRMMQKRKWMD--FFGGKFKNFMLKRFFKKSWGKYREMPKVADKSFAKQWEE 454 Query: 465 VR 466 ++ Sbjct: 455 MK 456 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: 763 Number of extensions: 33 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: 461 Length adjustment: 36 Effective length of query: 681 Effective length of database: 425 Effective search space: 289425 Effective search space used: 289425 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