Align Lactate utilization protein B (characterized)
to candidate 6938323 Sama_2442 iron-sulfur cluster-binding protein (RefSeq)
Query= SwissProt::O07021 (479 letters) >FitnessBrowser__SB2B:6938323 Length = 466 Score = 293 bits (750), Expect = 9e-84 Identities = 171/436 (39%), Positives = 242/436 (55%), Gaps = 21/436 (4%) Query: 34 LRTRRLEAAEELGNWEEWRSLSEEIRQHVLENLDFYLGQLAENVAKRGGHVYFAKTAEEA 93 LR +R AA L WE R+L +I+ H L L YL +G V++AK E Sbjct: 32 LREKRDRAASSLPEWETLRALGSQIKLHTLNQLPGYLEAFEAKCLSQGVKVHWAKDGAEH 91 Query: 94 SSYIRDVIQKKNGKKIVKSKSMVTEEINLNEVLEKEGCEVVETDLGEYILQIDDHDPPSH 153 + + D++ + KK+VKSKSM+TEE +LN LE +G EV++TDLGE I+Q+ +H PPSH Sbjct: 92 NRIVHDILSRHGVKKLVKSKSMLTEECHLNPFLEGKGIEVIDTDLGERIIQL-NHQPPSH 150 Query: 154 IVAPALHKNKEQIRDVFKERLDYQHTEK-PEELVMHARAILRKKFLEADIGITGCNFAIA 212 IV PA+H KE++ D+F E+L E P L ARA LR++FL AD +TG N A+A Sbjct: 151 IVVPAIHMKKEEVGDLFHEKLGTPKGESDPTRLTRAARAHLREQFLSADAAMTGVNMAVA 210 Query: 213 DTGSVSLVTNEGNGRLVSTLPKTQITVMGMERIVPSFSEFEVLVSMLTRSAVGQRLTSYI 272 G+V + TNEGN + + LPK Q+ MG+++IVP VL+ ML R+A GQ +T+Y Sbjct: 211 SEGAVIVCTNEGNADMGANLPKLQLHSMGIDKIVPDLDSAAVLLRMLARNATGQPITTYS 270 Query: 273 TALTGPKLEGEVDGPEEFHLVIVDNGRSNILGTE-FQSVLQCIRCAACINVCPVYRHVGG 331 + PK GE+ H++IVDNGRS ++ + L+CIRC C+N CPVYR GG Sbjct: 271 SLYRTPKPGGEM------HVIIVDNGRSAMMRDKLLGEALKCIRCGGCLNTCPVYRRSGG 324 Query: 332 HSYGSIYSGPIGAVLSPLLGGYDDYKELPYASSLCAACSEACPVKIPLHELLLKHRQNIV 391 +SYG GPIG + DD P+A +LC +CS CP K+PL +++ HR+ + Sbjct: 325 YSYGHTIPGPIGIAVG---ADEDDTHSSPWACTLCGSCSFVCPTKVPLDKIIF-HRRRLY 380 Query: 392 EKEGRAPISEKLAMKAFGLGASSLSLYKMGSKWAPAAM--TPFTEDEKISKGPGPLKNWT 449 + P + M G +S L G A A+ P + + +S W Sbjct: 381 AERKSLPYGKSGYMPLVGRFMASPLLLDTGMAAARIALKILPHSLLKPMSGA------WG 434 Query: 450 QIRDFPAPHKSRFRDW 465 + R+ PA S F W Sbjct: 435 KYRELPAAPGSSFEGW 450 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: 491 Number of extensions: 23 Number of successful extensions: 7 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: 466 Length adjustment: 33 Effective length of query: 446 Effective length of database: 433 Effective search space: 193118 Effective search space used: 193118 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 Apr 09 2024. 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