Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate AZOBR_RS25110 AZOBR_RS25110 (Fe-S)-binding protein
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__azobra:AZOBR_RS25110 Length = 474 Score = 278 bits (711), Expect = 4e-79 Identities = 179/471 (38%), Positives = 242/471 (51%), Gaps = 19/471 (4%) Query: 5 KTLKEYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDE-KAIIAEVADAKDHAAK 63 +T + K +L ++ LR + + RA F D E + A + A Sbjct: 3 ETSINFAKASSAALQDQQLRGNFRRAMDGLMSKRAVQFADTAEWNGVRTLGASVRLRALS 62 Query: 64 NMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNH 123 + L + +A K G++VH A T EAN I+ I + N K +K KSM +EE HLN Sbjct: 63 KLPELLEKLEANCTKNGIQVHWASTTDEANAIVLSIMQRVNAKLVVKGKSMVSEEMHLNA 122 Query: 124 RLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEV-DIQR 182 LE+ +E +E+DLGE+I+Q+ PSH++MPAIH++ Q+A LF + K+ + D+ + Sbjct: 123 FLEKHGIESLESDLGEYIVQLDEAMPSHIIMPAIHMNTKQIAHLFKQKIKEAEYTEDVAQ 182 Query: 183 LVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDK 242 L +ARR LR FATAD+GISG N AVAETGT+ LV NEGN R+ TT+P VH+A+ GL+K Sbjct: 183 LTDLARRVLRKKFATADVGISGVNMAVAETGTLCLVENEGNGRMSTTVPPVHIAVMGLEK 242 Query: 243 LVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALA 302 +V L D + +L R+AT Q IT+YV I + E DG E+H+V LDNGR + Sbjct: 243 VVEKLEDVPPVISLLTRSATAQPITTYVNMISSPRK-EGEKDGPNEIHLVILDNGRSGIY 301 Query: 303 EDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQN 362 D LRC+RCGAC N CPVY VGGH Y G IG IL G +K L Sbjct: 302 ADEELRNTLRCIRCGACMNHCPVYTKVGGHAYQAPYPGPIGSILMPQVEGLEKRGELPHA 361 Query: 363 CINCESCKHICAGGIDLPRLIKEIRARLNEEEGMPVETTLMGKMLKNRKLFHTLLRFAKW 422 C C +C IC + +P I EI RL E P G ++ + W Sbjct: 362 CTMCNACVEICP--VKIP--IVEIMGRLRSEAVHP------GDAVRGAGSHASKAEAMVW 411 Query: 423 AQKPVTGGTPYIRHLPQIFAKDHGFKALPAIADKPFRDEWETVRPRIAKPK 473 +T +P G A P A P EW VR AKP+ Sbjct: 412 KGWSMTYASPLAYQFATALLAKLG-NAAP--ASLPLLKEWTNVR---AKPR 456 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: 731 Number of extensions: 39 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: 474 Length adjustment: 36 Effective length of query: 681 Effective length of database: 438 Effective search space: 298278 Effective search space used: 298278 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