Align Uncharacterized protein (characterized, see rationale)
to candidate WP_043745482.1 AMB_RS20885 (Fe-S)-binding protein
Query= uniprot:E4PLR5 (279 letters) >NCBI__GCF_000009985.1:WP_043745482.1 Length = 249 Score = 252 bits (643), Expect = 6e-72 Identities = 123/245 (50%), Positives = 166/245 (67%), Gaps = 2/245 (0%) Query: 28 KPEAVTLFGTCVVDLFFPEAGLDTIRLLEREGVRVHFPQEQSCCGQPAWTSGYRDEAKAV 87 +PE+V FGTC++DLF+PEAGL + LL+REG++V FP Q+CCGQPA +GY+DEA+ V Sbjct: 6 RPESVYFFGTCLIDLFYPEAGLAGMELLQREGLKVVFPPNQTCCGQPARNNGYQDEARKV 65 Query: 88 ARAQLDILDRSGLPVVVPSGSCAGMFRHHYPALFADEPDTLKRVEALAERTFELTEFLLK 147 AR Q+D P+VVPSGSCAGM + HYP +F PD R A + R +ELTEFL+ Sbjct: 66 ARLQMDSFP-GDWPIVVPSGSCAGMMKTHYPEMFEGTPDH-DRAVAFSARVYELTEFLVD 123 Query: 148 VCRVQLADRGAPSKIALHTSCSARREMNTHLHARELLQQLEGVERIDHDHESECCGFGGT 207 V V+L D+G I H SC ++RE + LL+QL V +++ E ECCGFGG Sbjct: 124 VLGVKLVDKGQKVTITWHPSCHSQREAGVVEQPKALLRQLTNVTLVENPREKECCGFGGA 183 Query: 208 FSVRMPEVSGAMVKDKTRSLIDSGAVEMVTADGGCLMNINGSLEKQKESFRGRHLASFLW 267 F+VR E+S AMV DK S+ ++GA ++V+ D GCLMNI G+ EK + F+GRH+A F+ Sbjct: 184 FAVRQAEISAAMVTDKVASIEETGATQVVSGDCGCLMNITGAAEKAAKGFKGRHIAEFIL 243 Query: 268 ERTNG 272 ER +G Sbjct: 244 ERCHG 248 Lambda K H 0.320 0.134 0.406 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: 282 Number of extensions: 13 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: 279 Length of database: 249 Length adjustment: 25 Effective length of query: 254 Effective length of database: 224 Effective search space: 56896 Effective search space used: 56896 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 (21.8 bits) S2: 47 (22.7 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