Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate 208547 DVU3033 iron-sulfur cluster-binding protein
Query= uniprot:Q726S3 (717 letters) >MicrobesOnline__882:208547 Length = 717 Score = 1442 bits (3733), Expect = 0.0 Identities = 717/717 (100%), Positives = 717/717 (100%) Query: 1 MQNSKTLKEYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADAKDH 60 MQNSKTLKEYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADAKDH Sbjct: 1 MQNSKTLKEYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADAKDH 60 Query: 61 AAKNMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETH 120 AAKNMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETH Sbjct: 61 AAKNMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETH 120 Query: 121 LNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDI 180 LNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDI Sbjct: 121 LNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDI 180 Query: 181 QRLVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGL 240 QRLVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGL Sbjct: 181 QRLVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGL 240 Query: 241 DKLVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRA 300 DKLVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRA Sbjct: 241 DKLVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRA 300 Query: 301 LAEDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLV 360 LAEDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLV Sbjct: 301 LAEDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLV 360 Query: 361 QNCINCESCKHICAGGIDLPRLIKEIRARLNEEEGMPVETTLMGKMLKNRKLFHTLLRFA 420 QNCINCESCKHICAGGIDLPRLIKEIRARLNEEEGMPVETTLMGKMLKNRKLFHTLLRFA Sbjct: 361 QNCINCESCKHICAGGIDLPRLIKEIRARLNEEEGMPVETTLMGKMLKNRKLFHTLLRFA 420 Query: 421 KWAQKPVTGGTPYIRHLPQIFAKDHGFKALPAIADKPFRDEWETVRPRIAKPKLRIALFS 480 KWAQKPVTGGTPYIRHLPQIFAKDHGFKALPAIADKPFRDEWETVRPRIAKPKLRIALFS Sbjct: 421 KWAQKPVTGGTPYIRHLPQIFAKDHGFKALPAIADKPFRDEWETVRPRIAKPKLRIALFS 480 Query: 481 GCVQDFVYPEQMKAAVKVIASQNVDIDFPMDQSCCGLPVQMMGEREATIEVARQNVMAFD 540 GCVQDFVYPEQMKAAVKVIASQNVDIDFPMDQSCCGLPVQMMGEREATIEVARQNVMAFD Sbjct: 481 GCVQDFVYPEQMKAAVKVIASQNVDIDFPMDQSCCGLPVQMMGEREATIEVARQNVMAFD 540 Query: 541 AARYDYIVTLCASCASHLKETYPKLLTGHPEMTTRVRQFSNKIIDFSSFVHDVLGMKSDA 600 AARYDYIVTLCASCASHLKETYPKLLTGHPEMTTRVRQFSNKIIDFSSFVHDVLGMKSDA Sbjct: 541 AARYDYIVTLCASCASHLKETYPKLLTGHPEMTTRVRQFSNKIIDFSSFVHDVLGMKSDA 600 Query: 601 FKGGSNEKVAYHSSCHLCRGLGVVEQPRNLIAASGATYCKAEEEDVCCGFGGTFSAKFPE 660 FKGGSNEKVAYHSSCHLCRGLGVVEQPRNLIAASGATYCKAEEEDVCCGFGGTFSAKFPE Sbjct: 601 FKGGSNEKVAYHSSCHLCRGLGVVEQPRNLIAASGATYCKAEEEDVCCGFGGTFSAKFPE 660 Query: 661 LSAELLRKKLDNVEATGAGRLVADCPGCIMQLRGGMEKRGGKVKVGHVAELLAENLK 717 LSAELLRKKLDNVEATGAGRLVADCPGCIMQLRGGMEKRGGKVKVGHVAELLAENLK Sbjct: 661 LSAELLRKKLDNVEATGAGRLVADCPGCIMQLRGGMEKRGGKVKVGHVAELLAENLK 717 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: 1780 Number of extensions: 50 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: 717 Length adjustment: 40 Effective length of query: 677 Effective length of database: 677 Effective search space: 458329 Effective search space used: 458329 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: 55 (25.8 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