Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate AZOBR_RS23525 AZOBR_RS23525 ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__azobra:AZOBR_RS23525 Length = 269 Score = 251 bits (640), Expect = 1e-71 Identities = 132/246 (53%), Positives = 172/246 (69%), Gaps = 6/246 (2%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 +E+++++K +GS EVLK VSL +IG SGSGKST LRC N LE G+I +N Sbjct: 2 IEIRNVYKSFGSTEVLKDVSLTVPPSRTTVVIGPSGSGKSTLLRCCNCLETADRGEIRIN 61 Query: 64 NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123 + + DG K K+L +R+ MVFQ FNL+ HMT +EN+M APV V GM+K Sbjct: 62 HRTIIA----DG--KPLPDKELNALRAETGMVFQSFNLFPHMTTVENVMRAPVVVRGMAK 115 Query: 124 TEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183 EARE A L KVG+ + D YP +SGG++QR AIARALAM+P+VMLFDEPTSALDPE Sbjct: 116 AEARELAMELLRKVGLGDKADVYPSTLSGGQKQRAAIARALAMKPKVMLFDEPTSALDPE 175 Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243 LVG+VL+VM+ LA+EG TM+VVTHEMGFAREV++ +V + G + ESG+P ++ NP E Sbjct: 176 LVGEVLQVMKTLAEEGMTMMVVTHEMGFAREVADTVVVMADGRIVESGSPEQIFTNPTQE 235 Query: 244 RLQQFL 249 R + FL Sbjct: 236 RTRGFL 241 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: 193 Number of extensions: 4 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: 269 Length adjustment: 25 Effective length of query: 229 Effective length of database: 244 Effective search space: 55876 Effective search space used: 55876 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: 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