Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate Echvi_1568 Echvi_1568 Uncharacterized conserved protein containing a ferredoxin-like domain
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__Cola:Echvi_1568 Length = 457 Score = 227 bits (578), Expect = 1e-63 Identities = 138/376 (36%), Positives = 207/376 (55%), Gaps = 14/376 (3%) Query: 35 RASRANAFKDIDEKAIIAEVADA-KDHAAKNMDTLYAQFKAEAEKRGVKVHLARTAAEAN 93 R++R + + I E + + A A K++ ++ L QF+A A+ GV+V AR E N Sbjct: 31 RSNRDRSAQGIPEWETLRDTASATKNYVLSHLGELLEQFEANAKANGVEVLWARDDKEHN 90 Query: 94 EIIARIARDNNCKKAIKSKSMTAEETHLNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMV 153 E + RI ++N +KSKS+ EE LNH LE+ +V++TDLGE IIQ + PSH+V Sbjct: 91 EHVYRILQENKVSNIVKSKSILTEECGLNHYLEKKGYDVVDTDLGERIIQFAKQTPSHIV 150 Query: 154 MPAIHLSRYQVADLFSE-VTKQKQEVDIQRLVKVARRELRTHFATADMGISGANFAVAET 212 +PAIHL + + ++F + + +K D L + AR+ LR F A+ I+G NF +AET Sbjct: 151 LPAIHLKKQDIGEIFHDHIGTKKGASDPNYLTEAARQHLRKKFVEANAAITGVNFGIAET 210 Query: 213 GTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPTLHDALRSLKVLPRNATGQAITSYVTW 272 G + TNEGNA + T L VH+A G++KL+P D L++L R+ATGQ+IT+Y Sbjct: 211 GGFVVCTNEGNADMGTHLADVHIACMGIEKLIPRAADLGVFLRLLARSATGQSITNY--- 267 Query: 273 IGGANECEACVDGRKEMHIVFLDNGRRALAEDPLFSQVLRCVRCGACANVCPVYRLVGGH 332 ++ G+K ++I+ +DNGR A F L+C+RCGAC N CP+YR GGH Sbjct: 268 ---SSHFHRPAKGKK-LYIILVDNGRTAQLGREDFKNSLKCIRCGACMNTCPIYRRSGGH 323 Query: 333 KMGHIYIGAIGLILTYFFHGRD--KARNLVQNCINCESCKHICAGGIDLPRLIKEIRARL 390 + G IG IL+ GRD + L C SC +C I++ + + R + Sbjct: 324 SYNYTVPGPIGSILS---PGRDLKQYSTLPFASTLCGSCSDVCPVKINIHEQLYKWRQVI 380 Query: 391 NEEEGMPVETTLMGKM 406 E + L K+ Sbjct: 381 TENTNVDKSKQLSMKV 396 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: 723 Number of extensions: 31 Number of successful extensions: 4 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: 457 Length adjustment: 36 Effective length of query: 681 Effective length of database: 421 Effective search space: 286701 Effective search space used: 286701 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