Align ABC transporter for L-Lysine, ATPase component (characterized)
to candidate WP_152416156.1 C447_RS11610 ATP-binding cassette domain-containing protein
Query= reanno::pseudo5_N2C3_1:AO356_09895 (257 letters) >NCBI__GCF_000336675.1:WP_152416156.1 Length = 233 Score = 149 bits (377), Expect = 4e-41 Identities = 90/221 (40%), Positives = 124/221 (56%), Gaps = 11/221 (4%) Query: 9 EIRNLHKRYGQLEVLKGVSLTARDGDVISILGSSGSGKSTFLRCINLLENPNQGQILVAG 68 ++R + G +E L GVSL+ DG +++G SGSGKST L + L+ P G + VAG Sbjct: 5 DVRKTYDLGGTVEALAGVSLSLADGSYTAVMGPSGSGKSTLLNLVGALDTPTDGTVEVAG 64 Query: 69 EELKLKAAKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNIIEAPRRVLGQSKA 128 +L AA + E A G +EIGFVFQ FNL P ++N+ P G S+ Sbjct: 65 NDLG--AATDDERAAIRG-------TEIGFVFQTFNLLPRSDAVENVA-LPLVFAGWSRE 114 Query: 129 EAVEVAEALLAKVGIADKRHAYPAELSGGQQQRAAIARTLAMQPKVILFDEPTSALDPEM 188 E A LL +VG+ D+RH P +LSGGQ+QR AIAR LA P V+L DEPT +D E Sbjct: 115 RRHERATELLDRVGLGDRRHHRPTQLSGGQRQRVAIARALAPDPAVVLADEPTGNVDTET 174 Query: 189 VQEVLSVIRALAEEGRTMLLVTHEMGFARQVSSEVVFLHQG 229 V++++ A + G T+LLVTH A + +V + G Sbjct: 175 GAGVMNLLAAANDRGTTILLVTHSREIAEH-ADRIVTVRDG 214 Lambda K H 0.317 0.132 0.363 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: 116 Number of extensions: 4 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: 257 Length of database: 233 Length adjustment: 24 Effective length of query: 233 Effective length of database: 209 Effective search space: 48697 Effective search space used: 48697 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 (21.7 bits) S2: 46 (22.3 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