Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate CA265_RS18400 CA265_RS18400 iron-sulfur cluster-binding protein
Query= uniprot:E4PLR6 (483 letters) >FitnessBrowser__Pedo557:CA265_RS18400 Length = 461 Score = 346 bits (888), Expect = e-100 Identities = 168/361 (46%), Positives = 230/361 (63%) Query: 53 EGLRELGNRIKAGALSRLPDLLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQ 112 E ++ + IK + L L + E G KV WA EEA + II+ G Sbjct: 46 EASKKKAHVIKWRVMENLDKFLPEFESNFQRRGGKVIWANDAEEAQQEILNIIKRNNGKT 105 Query: 113 VVKGKSMVSEEMEMNDYLAERGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKL 172 V+K KSM +EE+ +ND+L + +E LESD+GEYIVQL + P HI+ PA+H +A +++L Sbjct: 106 VIKSKSMTTEEIHLNDFLEKNNIESLESDLGEYIVQLLGQAPYHIVTPAMHLSATDIAQL 165 Query: 173 FHDKLGEPETEDVNQLIQIGRRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMS 232 FHDK G P QL+Q R LR K++ AD+G+SG NF IA+TG++ L ENEGN R+S Sbjct: 166 FHDKFGTPIDATPPQLVQKARELLRDKYLNADIGISGGNFLIADTGSIALTENEGNARLS 225 Query: 233 TTAPPVHIAVTGIEKVVPNLRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEE 292 TT P +HIA+ GIEKV+P++ D+ LL GQ +T Y ++SGPR+P+E DGPEE Sbjct: 226 TTFPKIHIAIVGIEKVIPSIADLDLFWPLLASHGTGQNLTVYNTILSGPRQPNETDGPEE 285 Query: 293 VHLVLLDNGRTGAFADAQMRQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITP 352 ++++LLDNGRT A RQ L CIRCGAC+N CPVY +GGHTY Y GPIG +ITP Sbjct: 286 MYVILLDNGRTNLLAQKDQRQGLYCIRCGACLNACPVYKNIGGHTYNTTYSGPIGSVITP 345 Query: 353 HMAGLDKVPDHPSASSLCGACGEVCPVKIPIPELLQRLRQENVKNPEQPQQVKGGGAKYS 412 H+ G+++ ASSLCG C EVCPVKI I ++L R++ E ++ + G + +S Sbjct: 346 HLKGMEEFKHLSYASSLCGKCSEVCPVKIDIHKMLLLNRRDAAAGHENGKKEEIGWSMFS 405 Query: 413 R 413 R Sbjct: 406 R 406 Lambda K H 0.317 0.135 0.403 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: 549 Number of extensions: 18 Number of successful extensions: 2 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: 483 Length of database: 461 Length adjustment: 33 Effective length of query: 450 Effective length of database: 428 Effective search space: 192600 Effective search space used: 192600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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