Align Lactate utilization protein B (characterized)
to candidate RR42_RS07435 RR42_RS07435 (Fe-S)-binding protein
Query= SwissProt::O07021 (479 letters) >FitnessBrowser__Cup4G11:RR42_RS07435 Length = 469 Score = 382 bits (982), Expect = e-110 Identities = 189/468 (40%), Positives = 295/468 (63%), Gaps = 3/468 (0%) Query: 3 MKIGTDAFKERVSQGIDNEFMRGAVSGAQERLRTRRLEAAEELGNWEEWRSLSEEIRQHV 62 M++ + FK R Q + ++ ++ + + T R +A ++ +++ R +E R Sbjct: 1 MQVRSMEFKARAGQKLADQRLQQNLKKLSTKFVTARADAIRDI-DFDATREALKERRDRA 59 Query: 63 LENLDFYLGQLAENVAKRGGHVYFAKTAEEASSYIRDVIQKKNGKKIVKSKSMVTEEINL 122 L+NLD +L EN +RG V FA+T +A+ + ++ QK KK++KSKSMVTEE+ L Sbjct: 60 LQNLDVWLATFEENATRRGATVLFAETTADAARLVAEIAQKHGVKKVIKSKSMVTEEMRL 119 Query: 123 NEVLEKEGCEVVETDLGEYILQIDDHDPPSHIVAPALHKNKEQIRDVFKERLDYQHTEKP 182 N+VL + G + +ETDLGEYILQI+D +PPSHI+AP +HK+KE+I D+F + Sbjct: 120 NQVLGEMGVQSIETDLGEYILQINDAEPPSHIIAPVVHKDKEEIADLFAKVHHKPRLTDI 179 Query: 183 EELVMHARAILRKKFLEADIGITGCNFAIADTGSVSLVTNEGNGRLVSTLPKTQITVMGM 242 E+ AR +LR +FL AD+G+TG NF IA+TGSV++VTNEGN + + +P+ + V G+ Sbjct: 180 SEMTREAREVLRPEFLSADMGVTGGNFIIAETGSVAVVTNEGNEGMCTVMPRVHVAVTGI 239 Query: 243 ERIVPSFSEFEVLVSMLTRSAVGQRLTSYITALTGPKLEGEVDGPEEFHLVIVDNGRSNI 302 E+++P+ + ++ +L RSA GQ +++Y + LTGP+ EGE DGPE + V+VD GRS + Sbjct: 240 EKVLPTLEDLATVMRLLPRSATGQAISNYFSLLTGPRAEGERDGPEHMYFVLVDGGRSGL 299 Query: 303 LGTEFQSVLQCIRCAACINVCPVYRHVGGHSYGSIYSGPIGAVLSPLLGGYDDYKELPYA 362 +G +FQ +L+CIRC AC+N CPVY+ +GGH+YG +Y GP+G+VL+P G + +LP A Sbjct: 300 IGGDFQDMLRCIRCGACMNHCPVYQKIGGHAYGWVYPGPMGSVLTPSYVGIANALDLPQA 359 Query: 363 SSLCAACSEACPVKIPLHELLLKHRQNIVEKEGRAPISEKLAMKAFGLGASSLSLYKMGS 422 ++LC C+ CP IPL +LL K R+ +E+ G P E+L ++ +G A LY + Sbjct: 360 ATLCGECNRVCPASIPLSDLLRKLREKQMER-GLRPWQERLGLQVWGFVARRPGLYAFAT 418 Query: 423 KWAPAAMTPFTEDEK-ISKGPGPLKNWTQIRDFPAPHKSRFRDWFADR 469 + + K I++ P + WT+ RD PAP FR+ + +R Sbjct: 419 RIGARLLARMGGSSKLIARLPMAGRGWTETRDLPAPSGRTFRELYKER 466 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: 489 Number of extensions: 16 Number of successful extensions: 3 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: 469 Length adjustment: 33 Effective length of query: 446 Effective length of database: 436 Effective search space: 194456 Effective search space used: 194456 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