Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate H281DRAFT_02904 H281DRAFT_02904 L-lactate dehydrogenase complex protein LldF
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__Burk376:H281DRAFT_02904 Length = 463 Score = 211 bits (536), Expect = 8e-59 Identities = 133/373 (35%), Positives = 188/373 (50%), Gaps = 11/373 (2%) Query: 28 DKFAVAYRASRANAFKDIDEKAIIAEVADA-KDHAAKNMDTLYAQFKAEAEKRGVKVHLA 86 DK R R I E + E+A K+H ++ QF A AE GV VH A Sbjct: 24 DKRLWDLREKRDAQAHGIAEWETLRELASGIKEHTLSHLSEYLEQFAASAEANGVVVHWA 83 Query: 87 RTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLEEDNVEVIETDLGEWIIQMRH 146 TA E N ++ +I + +KSKSM +E + LE + V+ETDLGE I Q+ H Sbjct: 84 ATAEEHNALVHKIMSERGMTTLVKSKSMLTDECKMREYLEPRGITVMETDLGERIQQLDH 143 Query: 147 EGPSHMVMPAIHLSRYQVADLFSE-VTKQKQEVDIQRLVKVARRELRTHFA-TADMGISG 204 + PSHMV+PA+H R VA+LF + DI L + R R +F G++G Sbjct: 144 QDPSHMVVPAVHKLRADVAELFGRTIGTDPHNSDIHYLAESQRMNTRPYFVREKTAGMTG 203 Query: 205 ANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPTLHDALRSLKVLPRNATGQ 264 NFAVAETGT+ + TNEGNA L +P +H+A G++KL+P + D +++L R+A G Sbjct: 204 CNFAVAETGTVVVCTNEGNADLSANVPPLHIASIGIEKLIPKVSDLGVFIRMLSRSALGS 263 Query: 265 AITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALAEDPLFSQVLRCVRCGACANVCP 324 IT Y + EMH + +D+GR F L+C+RCGAC N CP Sbjct: 264 PITQYTSHFRAPRP-------GTEMHFILVDHGRSERLAMDDFWYSLKCIRCGACMNTCP 316 Query: 325 VYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINCESCKHICAGGIDLPRLIK 384 VYR GG G Y G IG I+ F + + + +N SC ++C I++ I Sbjct: 317 VYRRSGGLSYGGTYSGPIGAIINPTFDLKRYSALPFASTLN-GSCTNVCPVKINIHEQIY 375 Query: 385 EIRARLNEEEGMP 397 + R + E +P Sbjct: 376 KWRTVIAERHEVP 388 Lambda K H 0.321 0.135 0.402 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: 691 Number of extensions: 39 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: 717 Length of database: 463 Length adjustment: 36 Effective length of query: 681 Effective length of database: 427 Effective search space: 290787 Effective search space used: 290787 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 53 (25.0 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