Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate Ac3H11_3200 Amino acid ABC transporter permease protein
Query= reanno::pseudo3_N2E3:AO353_03040 (254 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3200 Length = 604 Score = 227 bits (579), Expect = 4e-64 Identities = 123/248 (49%), Positives = 172/248 (69%), Gaps = 1/248 (0%) Query: 3 KLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILL 62 ++ + + KRYG+ EVLK V+L G V I+G SGSGKST LR IN LE+ G I + Sbjct: 355 EVTIHGVSKRYGALEVLKDVTLTVLPGSVTVILGPSGSGKSTLLRSINHLERVDGGFIAI 414 Query: 63 NNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122 + E + + D + + L+R R + MVFQ+FNL+ H+T +ENI+EAPV V ++ Sbjct: 415 DGELIGYRQDADALYELGENDILKR-RVDVGMVFQNFNLFPHLTVLENIVEAPVTVRKLA 473 Query: 123 KAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDP 182 +AEA A LA+VG+S + +YP +SGG+QQRVAIARALA++P+V+LFDEPTSALDP Sbjct: 474 RAEAEALALELLARVGLSDKAHSYPRQLSGGQQQRVAIARALALKPKVLLFDEPTSALDP 533 Query: 183 ELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQS 242 ELVG+VL V++ LA+ G T+V+VTHE+GFAREV++ +VF+ +G V E+G P +V P Sbjct: 534 ELVGEVLDVIKELARTGTTLVIVTHEIGFAREVADTVVFMEQGRVVETGTPAKVFSQPDH 593 Query: 243 ERLQQFLS 250 R FL+ Sbjct: 594 PRTAAFLA 601 Lambda K H 0.317 0.131 0.364 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: 322 Number of extensions: 12 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: 604 Length adjustment: 30 Effective length of query: 224 Effective length of database: 574 Effective search space: 128576 Effective search space used: 128576 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: 50 (23.9 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