Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate 14445 b0307 predicted amino acid dehydrogenase with NAD(P)-binding domain and ferridoxin-like domain (NCBI)
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__Keio:14445 Length = 475 Score = 278 bits (711), Expect = 4e-79 Identities = 150/393 (38%), Positives = 232/393 (59%), Gaps = 12/393 (3%) Query: 9 EYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAE----VADAKDHAAKN 64 +++ +++ +++ +R A+ A A + AN K +DE E A +DH N Sbjct: 9 DFKTRIRQQIEDPIMRKAV---ANAQQRIGANRQKMVDELGHWEEWRDRAAQIRDHVLSN 65 Query: 65 MDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHR 124 +D Q + + G V+ ART +A I ++A+ N +K +KSKSM EE +NH Sbjct: 66 LDAYLYQLSEKVTQNGGHVYFARTKEDATRYILQVAQRKNARKVVKSKSMVTEEIGVNHV 125 Query: 125 LEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDIQRLV 184 L++ ++VIETDLGE+I+Q+ + PSH+V+PAIH R+Q+ + E + + + Sbjct: 126 LQDAGIQVIETDLGEYILQLDQDPPSHVVVPAIHKDRHQIRRVLHERLGYEGPETPEAMT 185 Query: 185 KVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLV 244 R+++R F +A++GI+G NFAVAETG++ LVTNEGNAR+ TTLP+ H+A+ G++++ Sbjct: 186 LFIRQKIREDFLSAEIGITGCNFAVAETGSVCLVTNEGNARMCTTLPKTHIAVMGMERIA 245 Query: 245 PTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGR-RALAE 303 PT + + +L R+A G +T Y TW+ G E VDG +E H+V +DNGR LA Sbjct: 246 PTFAEVDVLITMLARSAVGARLTGYNTWLTGPREA-GHVDGPEEFHLVIVDNGRSEVLAS 304 Query: 304 DPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNC 363 + F VLRC+RCGAC N CP YR +GGH G IY G IG +++ G ++L C Sbjct: 305 E--FRDVLRCIRCGACMNTCPAYRHIGGHGYGSIYPGPIGAVISPLLGGYKDFKDLPYAC 362 Query: 364 INCESCKHICAGGIDLPRLIKEIRARLNEEEGM 396 C +C ++C I L +LI R R+ E+G+ Sbjct: 363 SLCTACDNVCPVRIPLSKLILRHR-RVMAEKGI 394 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: 762 Number of extensions: 35 Number of successful extensions: 5 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