Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate WP_027179902.1 G496_RS0114515 4Fe-4S dicluster domain-containing protein
Query= uniprot:Q726S3 (717 letters) >NCBI__GCF_000429985.1:WP_027179902.1 Length = 717 Score = 1048 bits (2711), Expect = 0.0 Identities = 506/717 (70%), Positives = 596/717 (83%) Query: 1 MQNSKTLKEYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADAKDH 60 MQ++K LK+YR +LQ+SL NEFLR AMD+F VAYR SRA AF D+DEKA+I+EVA AKD Sbjct: 1 MQDAKDLKQYRDQLQDSLQNEFLRTAMDRFVVAYRGSRAKAFADMDEKALISEVACAKDD 60 Query: 61 AAKNMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETH 120 AA +D+LYAQFK EAEKRG VHLA+TA EANEII RIA++ NC+ +KSKSMTAEET Sbjct: 61 AATRLDSLYAQFKEEAEKRGAVVHLAKTATEANEIIGRIAKEENCQNIVKSKSMTAEETL 120 Query: 121 LNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDI 180 LNH LE+ + V+ETDLGEWIIQ+RHEGPSHMVMPAIHLSR QV+DLF++VT KQ VDI Sbjct: 121 LNHHLEDLGLNVVETDLGEWIIQLRHEGPSHMVMPAIHLSRNQVSDLFTDVTGCKQGVDI 180 Query: 181 QRLVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGL 240 ++LVKVARRELR FA ADMGISG NFA+AETGTIGLVTNEGNARLVTTLPRVHVAL GL Sbjct: 181 EKLVKVARRELRQKFAEADMGISGGNFAIAETGTIGLVTNEGNARLVTTLPRVHVALMGL 240 Query: 241 DKLVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRA 300 DKL P LHDALR LKVLPRNATGQAITSYVTWI G+NEC A D RK++H VFLDNGR A Sbjct: 241 DKLTPKLHDALRVLKVLPRNATGQAITSYVTWITGSNECAAAEDNRKKVHFVFLDNGRSA 300 Query: 301 LAEDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLV 360 LA+DP+FSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGR+KA+NLV Sbjct: 301 LAKDPVFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGREKAKNLV 360 Query: 361 QNCINCESCKHICAGGIDLPRLIKEIRARLNEEEGMPVETTLMGKMLKNRKLFHTLLRFA 420 QNCINC +CK ICAGGIDLPRLIKEI + +EEG PV++TL+GK+LKNRKLFHTLLR A Sbjct: 361 QNCINCGACKEICAGGIDLPRLIKEIHVLIQDEEGSPVQSTLLGKLLKNRKLFHTLLRTA 420 Query: 421 KWAQKPVTGGTPYIRHLPQIFAKDHGFKALPAIADKPFRDEWETVRPRIAKPKLRIALFS 480 K+AQKPV ++RHLP IF+ +H F+ALP +A KPFRD W+ V+P++ KP L++ALFS Sbjct: 421 KYAQKPVARKDGFLRHLPMIFSPEHNFRALPTVAAKPFRDMWKDVKPKVDKPVLKVALFS 480 Query: 481 GCVQDFVYPEQMKAAVKVIASQNVDIDFPMDQSCCGLPVQMMGEREATIEVARQNVMAFD 540 GCVQDFVYPEQ A VK++ +NV +DFPMDQSCCGLPVQMMGE++A +EVA QNV AFD Sbjct: 481 GCVQDFVYPEQSVATVKMLEGRNVAVDFPMDQSCCGLPVQMMGEKKAAVEVAIQNVTAFD 540 Query: 541 AARYDYIVTLCASCASHLKETYPKLLTGHPEMTTRVRQFSNKIIDFSSFVHDVLGMKSDA 600 AA YDYI+T+CASCASHLK YPKL+ P +V+QF++K+IDFSSF++DVLG+ Sbjct: 541 AADYDYILTMCASCASHLKHNYPKLIGNEPGFEVKVQQFADKVIDFSSFMNDVLGLTEAD 600 Query: 601 FKGGSNEKVAYHSSCHLCRGLGVVEQPRNLIAASGATYCKAEEEDVCCGFGGTFSAKFPE 660 F KV YH+ CHLCRGL V + PR L+ SG Y + EEE+VCCGFGGT+S KFP+ Sbjct: 601 FSDTVGRKVTYHAPCHLCRGLEVKDAPRELMKKSGLQYIECEEEEVCCGFGGTYSMKFPK 660 Query: 661 LSAELLRKKLDNVEATGAGRLVADCPGCIMQLRGGMEKRGGKVKVGHVAELLAENLK 717 +S +LL KK+++V+ATGA L+ DCPGC+MQLRGG +K G ++V H+AE LAE K Sbjct: 661 MSQQLLEKKIEHVKATGADVLLTDCPGCVMQLRGGAKKMGLDIEVRHIAEALAERKK 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: 1558 Number of extensions: 75 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: 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 24 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