Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate Ac3H11_2553 Cell division transporter, ATP-binding protein FtsE (TC 3.A.5.1.1)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2553 Length = 265 Score = 234 bits (598), Expect = 1e-66 Identities = 123/250 (49%), Positives = 163/250 (65%), Gaps = 6/250 (2%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 + ++ L K +GSH VL G+ V+ +IG SGSGKSTFLRC N LEQP G + + Sbjct: 19 VRIRGLRKAFGSHVVLNGIDFDVLPSQVVVVIGPSGSGKSTFLRCCNGLEQPEGGSVEIC 78 Query: 64 NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123 L +DG + L +R + MVFQ FNL+ H++ ++N+ P + G+S+ Sbjct: 79 GRTLV----QDGRM--LPDHDLNALREEVGMVFQSFNLFPHLSVLDNVTLGPRKLRGLSR 132 Query: 124 TEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183 EA E+A+ L KVG+AH+ A P +SGG++QRVAIARALAMEP VMLFDEPTSALDPE Sbjct: 133 KEAEERAQALLTKVGLAHKAPAMPASLSGGQKQRVAIARALAMEPRVMLFDEPTSALDPE 192 Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243 LVG+VL+VM+ LA EG TM+VVTHEM FAREV + +V + G + E+G P + NP E Sbjct: 193 LVGEVLQVMKLLASEGMTMMVVTHEMDFAREVGDVVVVMDGGGIIEAGAPATIFTNPTQE 252 Query: 244 RLQQFLSGSL 253 R + FL L Sbjct: 253 RTRSFLQAVL 262 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: 210 Number of extensions: 6 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: 265 Length adjustment: 24 Effective length of query: 230 Effective length of database: 241 Effective search space: 55430 Effective search space used: 55430 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