Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate 208542 DVU3028 iron-sulfur cluster-binding protein
Query= uniprot:Q726S3 (717 letters) >MicrobesOnline__882:208542 Length = 422 Score = 199 bits (507), Expect = 2e-55 Identities = 121/419 (28%), Positives = 206/419 (49%), Gaps = 10/419 (2%) Query: 306 LFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTY---FFHGRDKARNLVQN 362 L ++ C++CG C VCPV+ K + G I L+ + + + Sbjct: 5 LDDHMVACMKCGMCQAVCPVFAET--MKEADVTRGKIALLENLAKEMVSDPEGVQEKLNK 62 Query: 363 CINCESCKHICAGGIDLPRLIKEIRARLNEEEGM-PVETTLMGKMLKNRKLFHTLLRFAK 421 C+ C SC C G+ + + R +N G+ PV+ ++ ML N KLF+ LL Sbjct: 63 CLLCGSCGANCPSGVKIMDIFLRARCIVNSYMGLSPVKKAILRGMLTNPKLFNALLDMGS 122 Query: 422 WAQKPVTGGTPYI--RHLPQIFAKDHGFKALPAIADKPFRDEWETVRPRIAKPKLRIALF 479 Q T + +I + G + +A K +++ K +++A F Sbjct: 123 VFQGLFTTKVNDLLGSSCSKILSPIIGDRHFVGLASKSLHSRIKSLDTPAGKSGVKVAFF 182 Query: 480 SGCVQDFVYPEQMKAAVKVIASQNVDIDFPMDQSCCGLPVQMMGEREATIEVARQNVMAF 539 GC+ D ++ A +KV + V + P +CCG+P G+R + ++ + N+ F Sbjct: 183 PGCLGDKMFTSVADACLKVFSHHGVGVYMPEGMACCGIPSLASGDRVSYDKLVKLNLDLF 242 Query: 540 DAARYDYIVTLCASCASHLKETYPKLLTGHP-EMTTRVRQFSNKIIDFSSFVHDVLGMKS 598 ++DY+VT CA+C + +KE +PK++ +P EM ++ + K +D ++FV DVLG+ Sbjct: 243 AKGKFDYLVTPCATCTATIKEIWPKMMGDYPFEMRKQIEELEKKTMDVNAFVVDVLGVTP 302 Query: 599 DAFKGGSNEKVAYHSSCHLCRGLGVVEQPRNLIAASGA-TYCKAEEEDVCCGFGGTFSAK 657 A N KV +H SCH+ + LGV QPRNLI + + E D CCG GG+F+ Sbjct: 303 AADAPKGNVKVTFHDSCHMKKSLGVTAQPRNLIRMNPKYDLVEMAECDRCCGSGGSFNLY 362 Query: 658 FPELSAELLRKKLDNVEATGAGRLVADCPGCIMQLRGGMEKRGGKVKVGHVAELLAENL 716 +LS ++ +K N+ +GA + CP C++Q+ + + G +V V H E+ A++L Sbjct: 363 HYDLSKQIGERKRQNIVDSGAQVVSTGCPACMLQMTDMLSQHGDRVAVKHCIEIYADSL 421 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: 708 Number of extensions: 39 Number of successful extensions: 7 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: 422 Length adjustment: 36 Effective length of query: 681 Effective length of database: 386 Effective search space: 262866 Effective search space used: 262866 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