Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate WP_027179906.1 G496_RS0114540 (Fe-S)-binding protein
Query= uniprot:Q726S3 (717 letters) >NCBI__GCF_000429985.1:WP_027179906.1 Length = 430 Score = 226 bits (577), Expect = 1e-63 Identities = 137/423 (32%), Positives = 220/423 (52%), Gaps = 23/423 (5%) Query: 306 LFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTY---FFHGRDKARNLVQN 362 L Q+ C++CG C VCPV+ K + G I L+ D+ + Sbjct: 14 LDDQMAACMKCGMCQAVCPVF--AESMKESDVTRGKIALLEKLAHEMVKDVDEVNEKLNR 71 Query: 363 CINCESCKHICAGGIDLPRLIKEIRARLNEEEGM-PVETTLMGKMLKNRKLFHTLLR--- 418 C+ C +C C G+ + + + R + +G+ PV+ + +L KLF+ L Sbjct: 72 CLLCGTCAANCPSGVKIMDIFMKARVIVTTYKGLSPVKKAIFKGLLDRPKLFNLLTDMGA 131 Query: 419 -----FAKWAQKPVTGGTPYIRHLPQIFAKDHGFKALPAIADKPFRDEWETVRPRIAKPK 473 F + A K + GT L + K H +A +PFR ++ ++ + Sbjct: 132 VFGSPFMRSADKTI--GTKSCALLTPLIGKRH----FMPLAKRPFRKDYPSLDTERGESG 185 Query: 474 LRIALFSGCVQDFVYPEQMKAAVKVIASQNVDIDFPMDQSCCGLPVQMMGEREATIEVAR 533 L++A F GCV D ++P A +KV+ V I P +Q+CCG+P G+ + + + R Sbjct: 186 LKVAFFPGCVVDKMFPHVGHAVIKVLNHHGVGIYLPENQACCGIPTLASGDLDTFLSLMR 245 Query: 534 QNVMAFDAARYDYIVTLCASCASHLKETYPKLL-TGHPEMTTRVRQFSNKIIDFSSFVHD 592 +NV AFD +DYIVT CA+C S +KET+PK+L + ++ +V++ ++K +D + F+ D Sbjct: 246 KNVEAFDGGYFDYIVTPCATCTSTIKETWPKMLDDANSDIKEKVQELADKAMDINQFLVD 305 Query: 593 VLGMKSDAFKGGSNEKVAYHSSCHLCRGLGVVEQPRNLIAAS-GATYCKAEEEDVCCGFG 651 V+G+K+ K G + V YH CHL + LGV QPR L+ A+ + + E + CCG G Sbjct: 306 VVGVKALDHKAG-GKVVTYHDPCHLQKSLGVAAQPRELLKANPDYEFKEMNEANRCCGNG 364 Query: 652 GTFSAKFPELSAELLRKKLDNVEATGAGRLVADCPGCIMQLRGGMEKRGGKVKVGHVAEL 711 G+F+ +LS ++ +K DNV A+GA + CP C+MQL + + GG V V HV E+ Sbjct: 365 GSFNLYHYDLSKKIGERKRDNVRASGADVVATGCPACMMQLGDLLSQSGGGVDVRHVLEI 424 Query: 712 LAE 714 AE Sbjct: 425 YAE 427 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: 777 Number of extensions: 43 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 717 Length of database: 430 Length adjustment: 36 Effective length of query: 681 Effective length of database: 394 Effective search space: 268314 Effective search space used: 268314 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 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