Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate 207247 DVU1782 iron-sulfur cluster-binding protein
Query= uniprot:Q726S3 (717 letters) >MicrobesOnline__882:207247 Length = 475 Score = 287 bits (735), Expect = 7e-82 Identities = 165/420 (39%), Positives = 231/420 (55%), Gaps = 10/420 (2%) Query: 4 SKTLKEYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADA-KDHAA 62 S T +++ + +L + LR RA R N F D +E + +A K A Sbjct: 3 SSTSIDFKGNVTGALADRQLRANFRSALDGLRAKRLNVFSDAEELDRMRVQGEANKRRAL 62 Query: 63 KNMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLN 122 + L Q + G+ VH A T EAN I+ I R ++ +K KSM +EE HLN Sbjct: 63 AQLPALLEQLEHRCTANGIIVHWAETTDEANRIVLDIMRSHDATTLVKGKSMVSEEMHLN 122 Query: 123 HRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDIQR 182 LE +E +ETDLGE+IIQ+ HE PSH+++PA+H +R QVA +F E + ++++ Sbjct: 123 AYLERHGIEALETDLGEFIIQLNHEPPSHIIVPAVHKNRQQVARIFHEKLGEPYVDEVEK 182 Query: 183 LVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDK 242 L +ARR LR F TA +G+SG NFA+AETGT+ LV NEGN R+ TT+P VH+AL GL+K Sbjct: 183 LNAIARRTLREKFRTAQVGLSGVNFAIAETGTLLLVENEGNGRMCTTVPPVHIALMGLEK 242 Query: 243 LVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALA 302 +V L D L++L +ATGQ +T+YV I + DG +E+H+V LDNGR + Sbjct: 243 VVERLEDVPPLLRLLTGSATGQLVTTYVNCITSPRK-PGEKDGPREVHLVILDNGRSRML 301 Query: 303 EDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQN 362 DP S+ L+C+RCG C N CPVY +GGH +Y G IG ILT G + L Sbjct: 302 ADPQLSRTLQCIRCGTCLNHCPVYVRIGGHAYDSVYPGPIGKILTPQIDGLARKGVLATA 361 Query: 363 CINCESCKHICAGGIDLPRLIKEIRARLNEEEGMPVETTLMGKMLKNRKLFHTLLRFAKW 422 C +C+ +C I +P L++ +R E P E + G K TL A W Sbjct: 362 SSLCNACEEVCPVRIPIPALLRRLR---RESYAPPGEGVVKGAGSK-----RTLFEKAVW 413 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: 751 Number of extensions: 27 Number of successful extensions: 3 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: 475 Length adjustment: 36 Effective length of query: 681 Effective length of database: 439 Effective search space: 298959 Effective search space used: 298959 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