Align ABC transporter for L-Asparagine and possibly other L-amino acids, periplasmic substrate-binding component (characterized)
to candidate Ac3H11_1955 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4770 (304 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1955 Length = 299 Score = 241 bits (614), Expect = 2e-68 Identities = 132/296 (44%), Positives = 178/296 (60%), Gaps = 4/296 (1%) Query: 6 HILGAAIAAALISTPVFAAELTGTLKKIKESGTITLGHRDASIPFSYIADASGKPVGYSH 65 H+L A+ A + A+ T TL KIK SG++TLG R++S SY +GK VG+ Sbjct: 4 HLLAIAVTALAAGSAF--AQATDTLAKIKASGSVTLGVRESS-GLSYTL-GNGKYVGFHT 59 Query: 66 DIQLKVVEALKKDLDMPNLQVKYNLVTSQTRIPLVQNGTVDLECGSTTNNVERQQQVDFS 125 ++ V+ ++K L +P L +KY VTSQ RIPLV NGTVDLECGSTTNN R + V F+ Sbjct: 60 EMGEIVLADVQKQLGLPKLDIKYQPVTSQNRIPLVTNGTVDLECGSTTNNAARLKDVSFA 119 Query: 126 VGIFEIGTRLLSKADSKYKDFPDLAGKNVVTTAGTTSERILKAMNADKQMGMNVISAKDH 185 V + R++ KA+S DL GK V TT GTTS + L+ + + KDH Sbjct: 120 VTTYVEEVRMVVKANSGITSIKDLNGKTVATTTGTTSVQTLRKHERAGGIDFKEVMGKDH 179 Query: 186 GESFQMLETGRAVAFMMDDALLAGEAAKAKKASDWAVTGTPQSYEIYGCMVRKGDEPFKK 245 +SF MLETGRA AF+MD ++LA +K+K +D+ + G + E CM+RK D FKK Sbjct: 180 ADSFLMLETGRAEAFVMDGSILAANISKSKSPADYKIVGEVLNVEPIACMLRKDDPAFKK 239 Query: 246 AVDDAIKATYASGEINKIYEKWFMQPIPPKGLNLNFPMSDELKALIAKPTDKAADD 301 AVDD+IK G + K+Y+KWFMQP+PP + + PMSD K A P DK +D Sbjct: 240 AVDDSIKRQIKDGSLAKLYDKWFMQPVPPANVKIGLPMSDATKEAWANPNDKPMED 295 Lambda K H 0.315 0.131 0.368 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: 230 Number of extensions: 11 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: 304 Length of database: 299 Length adjustment: 27 Effective length of query: 277 Effective length of database: 272 Effective search space: 75344 Effective search space used: 75344 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 (21.5 bits) S2: 48 (23.1 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