Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 8502075 DvMF_2788 ABC transporter related (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3435 (254 letters) >FitnessBrowser__Miya:8502075 Length = 243 Score = 219 bits (558), Expect = 4e-62 Identities = 116/249 (46%), Positives = 162/249 (65%), Gaps = 14/249 (5%) Query: 4 LEVQDLHKRYGSH-EVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILL 62 ++ +HK Y S VL+ ++L+ G+V+ I G SGSGKST +RCIN LE G I++ Sbjct: 2 IKFDHVHKWYASGLHVLQDITLEIKQGEVVVICGPSGSGKSTLIRCINKLEPIQKGHIVV 61 Query: 63 NNEELKLVANKDGALKAADPK-QLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGM 121 + ++ DP+ L +R+ + VFQ FNL+ HMT +ENI AP+ V Sbjct: 62 DGVDIN------------DPRTNLTMLRAEVGFVFQQFNLYPHMTVLENITLAPLLVRNT 109 Query: 122 SKTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALD 181 + EA + A L KV + + AYPG +SGG+QQRVAIAR LAM+P +MLFDEPTSALD Sbjct: 110 PRAEAEKTAMELLEKVNIPDKAGAYPGQLSGGQQQRVAIARGLAMKPRIMLFDEPTSALD 169 Query: 182 PELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQ 241 PE++ +VL VM+ LA+EG TMV VTHEMGFAREV+++++F+ +GV+ E P NP Sbjct: 170 PEMINEVLDVMRQLAREGMTMVCVTHEMGFAREVADRVIFMDQGVMVEENTPEAFFSNPV 229 Query: 242 SERLQQFLS 250 +R ++FLS Sbjct: 230 HDRTKEFLS 238 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: 177 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: 243 Length adjustment: 24 Effective length of query: 230 Effective length of database: 219 Effective search space: 50370 Effective search space used: 50370 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