Align Lactate utilization protein B (characterized)
to candidate Dsui_0126 Dsui_0126 (4Fe-4S) cluster-containing protein
Query= SwissProt::O07021 (479 letters) >FitnessBrowser__PS:Dsui_0126 Length = 479 Score = 377 bits (968), Expect = e-109 Identities = 196/481 (40%), Positives = 298/481 (61%), Gaps = 12/481 (2%) Query: 3 MKIGTDAFKERVSQGIDNEFMRGAVSGAQERLRTRRLEAAEEL------GNWEEWRSLSE 56 M++ + F+ R ++ + + ++ + GA++ R E G++E R + Sbjct: 1 MEVKSLQFRARAAERLADPALQSKLGGAKQLFVGGRARVVAEFDSVGQAGDFETLRGIGA 60 Query: 57 EIRQHVLENLDFYLGQLAENVAKRGGHVYFAKTAEEASSYIRDVIQKKNGKKIVKSKSMV 116 EIR L +LD +L G V +A+ EA I D+ ++ KK++KSKSM+ Sbjct: 61 EIRDTALTDLDAWLEAFEAKATATGATVLWARDGREAQQLIVDIAKRHGVKKVIKSKSML 120 Query: 117 TEEINLNEVLEKEGCEVVETDLGEYILQIDDHDPPSHIVAPALHKNKEQIRDVFKERLDY 176 +EE LNE LE G + VETDLGEYILQ+ +PPSHI+APA+HKNKE++ ++F Sbjct: 121 SEEAGLNEGLEAAGVQSVETDLGEYILQLAK-EPPSHILAPAIHKNKEEVDELFARCHGR 179 Query: 177 QHTEKPE----ELVMHARAILRKKFLEADIGITGCNFAIADTGSVSLVTNEGNGRLVSTL 232 T + + L AR LR+ FL AD+GITG NF +A+TGSV+LVTNEGNGR+V+TL Sbjct: 180 PVTPEGQIDIPALTREARVALREHFLSADMGITGGNFLVAETGSVALVTNEGNGRMVTTL 239 Query: 233 PKTQITVMGMERIVPSFSEFEVLVSMLTRSAVGQRLTSYITALTGPKLEGEVDGPEEFHL 292 P+ + V+G+E+++P+ + L+ +LTRSA GQ +++Y++ LTGP+ EG V+GPE + Sbjct: 240 PRVHVAVVGIEKVIPTLEDLSALLRLLTRSATGQTISNYVSLLTGPRAEGAVEGPEHMYF 299 Query: 293 VIVDNGRSNILGTEFQSVLQCIRCAACINVCPVYRHVGGHSYGSIYSGPIGAVLSPLLGG 352 V++DNGR+ ++G +FQ +L+CIRC AC+N CPVY+ +GGH+YG +Y GP+G+VL+PL G Sbjct: 300 VLMDNGRAGLVGGDFQEMLRCIRCGACMNHCPVYQSIGGHAYGWVYPGPMGSVLTPLYTG 359 Query: 353 YDDYKELPYASSLCAACSEACPVKIPLHELLLKHRQNIVEKEGRAPISEKLAMKAFGLGA 412 + +LP A++LC CS CPVKIPL ELL K R+ +E E R P E+ A++ +G A Sbjct: 360 LEQAPDLPQAATLCGQCSIVCPVKIPLPELLRKLREKQMETELR-PWQERWALRTWGFFA 418 Query: 413 SSLSLYKMGSKWAPAAMTPFTEDEKISKGPGPLKNWTQIRDFPAPHKSRFRDWFADRETS 472 + LY + + A+ + + + W++ RDFPAP FR+ +A R Sbjct: 419 ARPRLYALAAGLGARALKLLAGGKASIRTLPGVPEWSRGRDFPAPQGKTFRELYAARRRQ 478 Query: 473 E 473 + Sbjct: 479 D 479 Lambda K H 0.316 0.134 0.390 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: 495 Number of extensions: 14 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: 479 Length of database: 479 Length adjustment: 34 Effective length of query: 445 Effective length of database: 445 Effective search space: 198025 Effective search space used: 198025 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