Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 209035 DVU0105 glutamine ABC transporter, ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >MicrobesOnline__882:209035 Length = 244 Score = 248 bits (633), Expect = 8e-71 Identities = 125/247 (50%), Positives = 177/247 (71%), Gaps = 13/247 (5%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 +E+++LHK YG H VL+G+ L G+V+ +IG SGSGKST LRCIN LE+ +G I+++ Sbjct: 5 IEIRNLHKSYGDHHVLRGIDLTVRTGEVVVVIGPSGSGKSTALRCINRLEEITSGTIIVD 64 Query: 64 NEELKLVANKDGALKAADPK-QLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122 +L DPK + +R+ MVFQ FNL+ HM+ +EN+ PV V M+ Sbjct: 65 GYDLY------------DPKTDINHVRTEAGMVFQQFNLFPHMSVLENVTIGPVKVRRMA 112 Query: 123 KTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDP 182 + EA+ L KVG+A + AYP +SGG++QRVAIAR+LAM+P+V+LFDEPTSALDP Sbjct: 113 RQEAQALGLALLEKVGLADKAHAYPDQLSGGQKQRVAIARSLAMQPKVLLFDEPTSALDP 172 Query: 183 ELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQS 242 ELVG+VL+VM+ LA+EG TMVVVTHEMGFAREV+++++F+ G ++E G P E+ +P++ Sbjct: 173 ELVGEVLEVMKQLAREGMTMVVVTHEMGFAREVADRVIFIDYGKIQEEGPPNELFADPKN 232 Query: 243 ERLQQFL 249 RL++FL Sbjct: 233 PRLREFL 239 Lambda K H 0.317 0.131 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: 199 Number of extensions: 7 Number of successful extensions: 2 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: 244 Length adjustment: 24 Effective length of query: 230 Effective length of database: 220 Effective search space: 50600 Effective search space used: 50600 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 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