Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate H281DRAFT_00473 H281DRAFT_00473 iron-sulfur cluster-binding protein
Query= uniprot:E4PLR6 (483 letters) >FitnessBrowser__Burk376:H281DRAFT_00473 Length = 471 Score = 358 bits (919), Expect = e-103 Identities = 198/464 (42%), Positives = 276/464 (59%), Gaps = 12/464 (2%) Query: 14 FRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDAD---EREGLRELGNRIKAGALSRL 70 F+ RA + LAD +L+ N ++ RA A D R L+E NR AL L Sbjct: 8 FKARAGQKLADQRLQQNLTKLSTKFVSARAVAMTAIDFAATRAALKERRNR----ALENL 63 Query: 71 PDLLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEMEMNDYL 130 LE E++ GV V +AET +EA LV I +V+K KSMV+EEM +N+ L Sbjct: 64 DVWLETFEREANRRGVTVLFAETTQEAARLVGDIARRHDVKKVIKTKSMVTEEMRLNEVL 123 Query: 131 AERGVECLESDMGEYIVQLD-NEKPSHIIMPAIHKNARQVSKLFHDKLGEPETEDVNQLI 189 + GV+ +E+D+GEYI+Q++ NE PSHII P +HK+ +++ LF G P ++ + Sbjct: 124 GQMGVQSIETDLGEYILQINGNEPPSHIIAPVVHKDKDEIADLFAKTHGRPRLTEIPDMT 183 Query: 190 QIGRRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTGIEKVV 249 R+ LR F+ AD+GV+G NF IAETG+++LV NEGN M T P VH+AVTGIEKV+ Sbjct: 184 LEARQVLRPHFLSADMGVTGGNFVIAETGSVVLVTNEGNEGMCTVMPRVHVAVTGIEKVL 243 Query: 250 PNLRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNGRTGAFADA 309 P L D+ + LL RSA GQ + Y +L++GPR + DGPE +++VL+D GRTG Sbjct: 244 PTLEDLATAMRLLPRSATGQTTSNYFSLLTGPRGEGDQDGPEHMYVVLVDGGRTGLIG-G 302 Query: 310 QMRQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVPDHPSASSL 369 ++ L CIRCGACMNHCPVY +VGGH YG VYPGP+G ++TP GLDK D P A++L Sbjct: 303 DFQEMLRCIRCGACMNHCPVYQKVGGHAYGWVYPGPMGSVLTPSYVGLDKALDLPQAATL 362 Query: 370 CGACGEVCPVKIPIPELLQRLRQENVKNPEQPQQVKGGGAKYSRTERWIWRGWQMLNTRP 429 CG C VCPV IP+ +LL++LR++ V+ +P + + G A + + G L T+ Sbjct: 363 CGECNSVCPVGIPLSDLLRKLREKQVERRLRPWKERAGLAVWGFMA--LHPGMYALVTKL 420 Query: 430 AL-YRSFLWAATRFRALAPKKAGPWTENHSAPVPARRSLHDLAA 472 A+ L + R A P WT+ P P R+ +L A Sbjct: 421 AVRVLERLGGSNRSIAKLPLAGAGWTDTRDMPAPVGRTFRELYA 464 Lambda K H 0.317 0.135 0.403 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: 531 Number of extensions: 18 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: 483 Length of database: 471 Length adjustment: 33 Effective length of query: 450 Effective length of database: 438 Effective search space: 197100 Effective search space used: 197100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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