Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate 8501132 DvMF_1868 protein of unknown function DUF162 (RefSeq)
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__Miya:8501132 Length = 716 Score = 1236 bits (3199), Expect = 0.0 Identities = 602/717 (83%), Positives = 665/717 (92%), Gaps = 1/717 (0%) Query: 1 MQNSKTLKEYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADAKDH 60 MQ +KTLKEYRKEL+ESLDNEFLR AMDKFA AY SRANAF+ +DEKA+IAEVADAKD Sbjct: 1 MQTAKTLKEYRKELRESLDNEFLREAMDKFATAYPVSRANAFRGLDEKAMIAEVADAKDA 60 Query: 61 AAKNMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETH 120 AAKNMD LYAQFKAEA+KRGVKVH+A+ AAEANEIIARIA+++NCKK +KSKSMTAEET Sbjct: 61 AAKNMDALYAQFKAEAKKRGVKVHMAKDAAEANEIIARIAKNSNCKKIVKSKSMTAEETL 120 Query: 121 LNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDI 180 LNHRLEED +EVIETDLGEWIIQ+RHEGP+HMVMPAIHLSRYQVADLFSEVTKQKQEVDI Sbjct: 121 LNHRLEEDGLEVIETDLGEWIIQLRHEGPTHMVMPAIHLSRYQVADLFSEVTKQKQEVDI 180 Query: 181 QRLVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGL 240 QRLVKVARRELR HFATADMGISGANFA+AE+GTIGLVTNEGNARLVTTLPRVHVAL GL Sbjct: 181 QRLVKVARRELRQHFATADMGISGANFAIAESGTIGLVTNEGNARLVTTLPRVHVALCGL 240 Query: 241 DKLVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRA 300 DKL P+L+DAL+SL+VLPRNATGQAITSYVTWI GANEC+A D +KEMHIVFLDNGRRA Sbjct: 241 DKLTPSLNDALKSLRVLPRNATGQAITSYVTWITGANECKAAADEKKEMHIVFLDNGRRA 300 Query: 301 LAEDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLV 360 LA+DPLFSQV+RCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHG+DKARNLV Sbjct: 301 LAQDPLFSQVMRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGKDKARNLV 360 Query: 361 QNCINCESCKHICAGGIDLPRLIKEIRARLNEEEGMPVETTLMGKMLKNRKLFHTLLRFA 420 QNCINCESCK ICAGGIDLPRLIKEIRARL+EE+G PVE TL+GK+LKNRKLFHTLLRF Sbjct: 361 QNCINCESCKSICAGGIDLPRLIKEIRARLSEEDGAPVEATLLGKVLKNRKLFHTLLRFG 420 Query: 421 KWAQKPVTGGTPYIRHLPQIFAKDHGFKALPAIADKPFRDEWETVRPRIAKPKLRIALFS 480 K+AQKPVTGGTPY+RHLPQ+F KDHGF+ALPAIADK FRDEWET+RPR++ KLR+ALFS Sbjct: 421 KFAQKPVTGGTPYLRHLPQMFMKDHGFRALPAIADKAFRDEWETIRPRVSNAKLRVALFS 480 Query: 481 GCVQDFVYPEQMKAAVKVIASQNVDIDFPMDQSCCGLPVQMMGEREATIEVARQNVMAFD 540 GCVQDFVYPEQMKAAVKV+AS+ V++DFPMDQSCCGLPVQMM ER+ATI+VARQNVMAFD Sbjct: 481 GCVQDFVYPEQMKAAVKVLASRGVEMDFPMDQSCCGLPVQMMAERQATIDVARQNVMAFD 540 Query: 541 AARYDYIVTLCASCASHLKETYPKLLTGHPEMTTRVRQFSNKIIDFSSFVHDVLGMKSDA 600 AA+YDYI+TLCASCASHLKE YP +L G +MT +V+ F++K+IDFSSFVHDVLGM +D Sbjct: 541 AAKYDYILTLCASCASHLKEGYPNILAGQTDMTGKVKLFASKVIDFSSFVHDVLGMTADD 600 Query: 601 FKGGSNEKVAYHSSCHLCRGLGVVEQPRNLIAASGATYCKAEEEDVCCGFGGTFSAKFPE 660 FK G EKVAYHSSCHLCRGLGVVEQPR LIA+SG+ YC A+EE VCCGFGGTFS KFPE Sbjct: 601 FK-GKGEKVAYHSSCHLCRGLGVVEQPRALIASSGSEYCPAQEEAVCCGFGGTFSMKFPE 659 Query: 661 LSAELLRKKLDNVEATGAGRLVADCPGCIMQLRGGMEKRGGKVKVGHVAELLAENLK 717 LS ELL KKL+N EATGA R+VADCPGCIMQ+RGG EKRG ++KVGH+AELLAENLK Sbjct: 660 LSKELLDKKLNNAEATGATRMVADCPGCIMQIRGGAEKRGSRMKVGHIAELLAENLK 716 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: 1609 Number of extensions: 63 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: 716 Length adjustment: 40 Effective length of query: 677 Effective length of database: 676 Effective search space: 457652 Effective search space used: 457652 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 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