Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_011384082.1 AMB_RS08465 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_000009985.1:WP_011384082.1 Length = 253 Score = 229 bits (585), Expect = 3e-65 Identities = 110/251 (43%), Positives = 170/251 (67%), Gaps = 1/251 (0%) Query: 1 MALLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTV 60 M+LL+V++L+K FGG+ AV D+T + G + +IGPNGAGKTTLFNL+TGVY PS G V Sbjct: 1 MSLLKVEKLSKEFGGVHAVEDLTFSVEAGHIHSIIGPNGAGKTTLFNLITGVYTPSSGRV 60 Query: 61 TLDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPA 120 L++G PY++A LG+ RTFQN+++F ++ ++NV++ H + S LRLP Sbjct: 61 LFQDRLVSGMKPYELAELGMSRTFQNLQIFFNMQAIENVMVGHHLHLDRRFLPSLLRLPK 120 Query: 121 FYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAA 180 + ++E + L++ L + A ++ YG +RLEI RALA +PK+L LDEPAA Sbjct: 121 VTRRDRECREYCAGLMEFVGLGKYLDADAASMPYGALKRLEIARALAAQPKLLLLDEPAA 180 Query: 181 GMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIK 240 G+N E+ E+ E+I+++ +T++L+EHDM +VM ++++I L+YGR +A+GTP E++ Sbjct: 181 GLNATESREIDEVIKKVATT-GVTVVLVEHDMKMVMGISDQITALDYGRKLAEGTPAEVR 239 Query: 241 TNKRVIEAYLG 251 N V+ AYLG Sbjct: 240 ANPEVVSAYLG 250 Lambda K H 0.319 0.139 0.385 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: 175 Number of extensions: 6 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: 254 Length of database: 253 Length adjustment: 24 Effective length of query: 230 Effective length of database: 229 Effective search space: 52670 Effective search space used: 52670 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 (21.7 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