Align Lactate utilization protein B (characterized)
to candidate YP_428686.1 Rru_A3605 iron-sulfur cluster binding protein
Query= SwissProt::O07021 (479 letters) >NCBI__GCF_000013085.1:YP_428686.1 Length = 472 Score = 355 bits (912), Expect = e-102 Identities = 181/460 (39%), Positives = 272/460 (59%), Gaps = 6/460 (1%) Query: 9 AFKERVSQGIDNEFMRGAVSGAQERLRTRRLEAAEELGNWEEWRSLSEEIRQHVLENLDF 68 AFK+ + + ++ + A+ + R R EA L ++ R +++ HVL+NLDF Sbjct: 7 AFKDNARKALTDDTLASALGTMKAGFRRARAEAIGRLPEFDALRDAGRDLKNHVLDNLDF 66 Query: 69 YLGQLAENVAKRGGHVYFAKTAEEASSYIRDVIQKKNGKKIVKSKSMVTEEINLNEVLEK 128 YL V +GGHV++ + A EA I + + K + K KSM+TEEI LN LE Sbjct: 67 YLETFEAKVIAQGGHVHWCRDAAEARETILAICRDSGAKTVTKGKSMITEEIGLNAYLEA 126 Query: 129 EGCEVVETDLGEYILQIDDHDPPSHIVAPALHKNKEQIRDVFKERLDY----QHTEKPEE 184 G +ETDLGEYI+Q+ + PSHIVAPA+H + + + F++ + E+ + Sbjct: 127 NGVTPIETDLGEYIIQLRG-ETPSHIVAPAIHLRRPHVAEAFRKAHTQFAADRRLEEHRD 185 Query: 185 LVMHARAILRKKFLEADIGITGCNFAIADTGSVSLVTNEGNGRLVSTLPKTQITVMGMER 244 + ARA++R FL AD+GITG N IA+TGS +VTNEGNG L LP+ + V +E+ Sbjct: 186 FLDEARAVMRGNFLAADVGITGANMMIAETGSTVIVTNEGNGDLTQLLPRVHVVVASLEK 245 Query: 245 IVPSFSEFEVLVSMLTRSAVGQRLTSYITALTGPKLEGEVDGPEEFHLVIVDNGRSNILG 304 IVP+ + +++ +L RSA GQ +++Y T TGP+ +VDGP+ FH+V++DNGRS++LG Sbjct: 246 IVPTLDDAALVLRLLARSASGQDMSAYTTFSTGPRRPDDVDGPDAFHVVLLDNGRSDMLG 305 Query: 305 TEFQSVLQCIRCAACINVCPVYRHVGGHSYGSIYSGPIGAVLSPLLGGYDDYKELPYASS 364 T FQ +L+CIRCAAC+N CPVY +GGH+YG +Y GP+G+VL+P L G + +LP AS+ Sbjct: 306 TGFQEMLRCIRCAACMNHCPVYGAIGGHAYGWVYPGPMGSVLTPALIGLEQAADLPNAST 365 Query: 365 LCAACSEACPVKIPLHELLLKHRQNIVEKEGRAPISEKLAMKAFGLGASSLSLYKMGSKW 424 LC C E CP++IPL +L R+ E+ P + + A+ A+ LY++ ++ Sbjct: 366 LCGRCEEVCPMRIPLPRMLRHWREKEFERH-LTPKPARFGLGAWAFVAARPGLYRLTTRL 424 Query: 425 APAAMTPFTEDEKISKGPGPLKNWTQIRDFPAPHKSRFRD 464 A++ + G WT +R PAP F D Sbjct: 425 IAGALSRLGGKRGHLRSLGLANGWTAVRAMPAPEGRTFMD 464 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: 511 Number of extensions: 16 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: 472 Length adjustment: 33 Effective length of query: 446 Effective length of database: 439 Effective search space: 195794 Effective search space used: 195794 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 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