Align Lactate utilization protein B (characterized)
to candidate WP_013076353.1 BTUS_RS12080 iron-sulfur cluster-binding protein
Query= SwissProt::O07021 (479 letters) >NCBI__GCF_000092905.1:WP_013076353.1 Length = 480 Score = 470 bits (1210), Expect = e-137 Identities = 233/464 (50%), Positives = 315/464 (67%), Gaps = 4/464 (0%) Query: 3 MKIGTDAFKERVSQGIDNEFMRGAVSGAQERLRTRRLEAAEELGNWEEWRSLSEEIRQHV 62 M + + KER ++ + N+F+R AV ++ + A LG+WE WR IR H Sbjct: 1 MTVPSATMKERAAEALHNDFLREAVKITTDKFFAGKTLAQRSLGDWEAWRERGRAIRAHA 60 Query: 63 LENLDFYLGQLAENVAKRGGHVYFAKTAEEASSYIRDVIQKKNGKKIVKSKSMVTEEINL 122 L +LD+YLGQL + V GG V+ +TAE+A I ++ + +N + ++KSKSMVTEEI+L Sbjct: 61 LAHLDYYLGQLIDQVKSLGGKVHLCETAEDAVQVIVEIARARNARSVIKSKSMVTEEIHL 120 Query: 123 NEVLEKEGCEVVETDLGEYILQIDDHDPPSHIVAPALHKNKEQIRDVFKERLDYQHTEKP 182 N+ LE G VETDLGEYI+Q+ H+ PSHI+APA+HK ++ + ++F + + Sbjct: 121 NKALEAIGVRAVETDLGEYIIQLA-HETPSHIIAPAIHKTRKDVAELFSQVAGRPIEDDT 179 Query: 183 EELVMHARAILRKKFLEADIGITGCNFAIADTGSVSLVTNEGNGRLVSTLPKTQITVMGM 242 + L AR LR++FL DIGITGCNFA+A+TGSV+L TNEGNGR+V+TLP + VMGM Sbjct: 180 DTLTNFARQKLREEFLNGDIGITGCNFAVAETGSVALFTNEGNGRMVTTLPPVHVAVMGM 239 Query: 243 ERIVPSFSEFEVLVSMLTRSAVGQRLTSYITALTGPKLEGEVDGPEEFHLVIVDNGRSNI 302 ER+VP+F + EV++++L RS GQ+LTSY+T +TGP+ EGEVDGPEEFHLVI+DNGRS I Sbjct: 240 ERVVPTFEDLEVMMNLLPRSGTGQKLTSYVTVITGPRREGEVDGPEEFHLVILDNGRSRI 299 Query: 303 L-GTEFQSVLQCIRCAACINVCPVYRHVGGHSYGSIYSGPIGAVLSPLL-GGYDDYKELP 360 L EF+ LQCIRC AC+NVCPVYR +GGH+YG +Y GPIGAV++PLL D + +LP Sbjct: 300 LRDPEFREALQCIRCGACLNVCPVYRQIGGHAYGWVYPGPIGAVITPLLTDDLDRWGDLP 359 Query: 361 YASSLCAACSEACPVKIPLHELLLKHRQNIVEKEGRAPISEKLAMKAFGLGASSLSLYKM 420 YASSLCAAC+EACPVKIPLH++L++HR V G+ P E++A + + +S Y+ Sbjct: 360 YASSLCAACAEACPVKIPLHDMLVRHRVRYV-AAGKTPPVERVAFRLYKRAFTSPRRYRR 418 Query: 421 GSKWAPAAMTPFTEDEKISKGPGPLKNWTQIRDFPAPHKSRFRD 464 K A P +D +S L WT RDFPA RFRD Sbjct: 419 ALKTAVTFQRPLVKDRHLSARLPGLAGWTAGRDFPAAAPKRFRD 462 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: 539 Number of extensions: 21 Number of successful extensions: 6 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: 480 Length adjustment: 34 Effective length of query: 445 Effective length of database: 446 Effective search space: 198470 Effective search space used: 198470 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