Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate SM_b21138 SM_b21138 amino acid ABC transporter ATP-binding protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__Smeli:SM_b21138 Length = 255 Score = 262 bits (670), Expect = 4e-75 Identities = 133/249 (53%), Positives = 184/249 (73%), Gaps = 1/249 (0%) Query: 4 LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63 LE++DLHKRYG+ EVLKGV G+VISIIGSSGSGK+T LRCIN+LE+ G I ++ Sbjct: 5 LEIRDLHKRYGTVEVLKGVDCSMRQGEVISIIGSSGSGKTTMLRCINMLEEFQGGTIAID 64 Query: 64 NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123 +E+ GA + +++ R R+ M FQ FNL+ HMTA N+M V V MS+ Sbjct: 65 GQEIGY-ETAGGARRRKPEREIARQRALTGMAFQQFNLFPHMTAAANVMLGLVKVKKMSR 123 Query: 124 TEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183 EAR AE +L++VG+ RKD YPG +SGG+QQRVAIARA+AM P++MLFDE TSALDPE Sbjct: 124 DEARVLAEKWLDRVGLLSRKDHYPGQLSGGQQQRVAIARAIAMNPKLMLFDEVTSALDPE 183 Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243 LV +VL+V++ LA++G +M++VTHEM FA EVS++++F+++G + E G+PRE+ + P++E Sbjct: 184 LVNEVLQVIKGLAEDGMSMLIVTHEMRFAYEVSSRVIFMNQGRIGEEGHPREMFLKPRTE 243 Query: 244 RLQQFLSGS 252 RL +FL S Sbjct: 244 RLAEFLKTS 252 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: 196 Number of extensions: 5 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: 255 Length adjustment: 24 Effective length of query: 230 Effective length of database: 231 Effective search space: 53130 Effective search space used: 53130 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