Align Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale)
to candidate RR42_RS20120 RR42_RS20120 amino acid ABC transporter substrate-binding protein
Query= uniprot:G8ALJ3 (366 letters) >FitnessBrowser__Cup4G11:RR42_RS20120 Length = 383 Score = 203 bits (517), Expect = 5e-57 Identities = 124/370 (33%), Positives = 200/370 (54%), Gaps = 11/370 (2%) Query: 3 YKLSLLVAVAATAMTASVAK----ADIAVATAGPITGQYATFGEQMKKGIEQAVADINAA 58 +K +L VA++ + A+ A +I + A P+TG A +G+ M+ G+ A+ ++NA Sbjct: 6 HKTALTVALSVAGLCATSAAFAQAQEIKLGFAAPMTGGQAQYGKDMQNGVVLAIEEMNAT 65 Query: 59 GGVLGQK---LKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEG 115 +G K L DDA DPK VA +L G++ + GHF SG+SIPAS VY G Sbjct: 66 KPKIGGKDVKFVLLSEDDAADPKTGSVVAQKLVDNGIQGMLGHFNSGTSIPASMVYNRAG 125 Query: 116 VLQISPASTNPKLTEQNLKNVFRVCGRDDQQGQIAGKYLLENYKGKNVAILHDKSAYGKG 175 + QI+ A T P+ T Q K FR+ D QQG + G ++++ KN+AI+ D++AYG+G Sbjct: 126 IPQIAMA-TAPEYTRQGFKTTFRMMTSDTQQGSVIGAFVVKKLGAKNIAIVDDRTAYGQG 184 Query: 176 LADETQKALNAGGQKEKIYEAYTAGEKDYSALVSKLKQEAVDVVYVGGYHTEAGLLARQM 235 LADE +KA A G K E D+ A+++ +K+ DV++ GG T++ +A+Q+ Sbjct: 185 LADEFEKAAKAAGGKIVRREFTNDKAVDFKAVLTNIKRSNPDVIFFGGAETQSAPMAKQV 244 Query: 236 KDQGLNAPIVSGDALVTNEYWAITGPAGENTMMTFGPDPREMPEAKEAVEK--FRKAGYE 293 K+ G+ +P+VSG+ T+ + + GPA E T+++ P E A EK ++ G + Sbjct: 245 KELGMKSPVVSGEMSKTDNFLKLAGPAAEGTVVSLAGLPLEQMPGGTAYEKKYEKRFGSK 304 Query: 294 PEGYTLYTYAALQIWAEAAKQANSTDSAKIADVLRKNSYNTVIGK-IGFDAKGDVTSPAY 352 + Y+ Y Y A +A S D A+ VL + V K + +DA+GD+ Sbjct: 305 VQTYSPYAYDGATALMTAMIKAGSADPARYLPVLAATNMQGVTTKTLAYDARGDLKDGGI 364 Query: 353 VWYRWNNGQY 362 Y+ G++ Sbjct: 365 TVYKVVGGKW 374 Lambda K H 0.312 0.129 0.366 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: 336 Number of extensions: 21 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: 366 Length of database: 383 Length adjustment: 30 Effective length of query: 336 Effective length of database: 353 Effective search space: 118608 Effective search space used: 118608 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 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