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) >lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3200 Amino acid ABC transporter permease protein 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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