Align glutamate-aspartate periplasmic-binding protein (characterized)
to candidate Ac3H11_1603 Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
Query= CharProtDB::CH_002441 (302 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1603 Length = 305 Score = 214 bits (546), Expect = 2e-60 Identities = 121/298 (40%), Positives = 175/298 (58%), Gaps = 17/298 (5%) Query: 14 ALSAGLAQAD-DAAPAAGST-----LDKIAKNGVIVVGHRESSVPFSY-YDNQQKVVGYS 66 AL+AGL A APA T L+KI +G V+G RE+S P +Y +K VGY Sbjct: 10 ALAAGLTLACLTTAPALAQTVTQPTLEKIKASGKAVLGVRETSPPMAYALGANEKYVGYH 69 Query: 67 QDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAF 126 + +++ + PD +++ + +T+QN +PL+QNGT D CG TTNN RQ+Q AF Sbjct: 70 VELCERVLKEIA-----PDAKLEYMAVTAQNTLPLVQNGTLDIGCGPTTNNTARQQQVAF 124 Query: 127 SDTIFVVGTRLLTKKGGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMN---MRIIS 183 + T +V R+ +K D+K L + + ++GTT+ LL K +E+ + ++ + Sbjct: 125 AVTTYVSEVRMAVRKDSDLKSINQLAGRTIAASTGTTAVQLLRK--QERVLGGAPIKTVL 182 Query: 184 AKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDP 243 KDH +SF LESGRA AF++DD LLAG A +K P + IVG+P E + RKDDP Sbjct: 183 GKDHHESFLLLESGRADAFVLDDNLLAGMIANSKDPSAYRIVGEPLGAEPIALLFRKDDP 242 Query: 244 QFKKLMDDTIAQVQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDKAL 301 FK +D + ++ SGE EK + KWF NPIPPKN+++N L ++ LF PNDK L Sbjct: 243 TFKAAVDGVLTKLMQSGEMEKIYTKWFVNPIPPKNMSLNLPLGTTLRQLFATPNDKPL 300 Lambda K H 0.314 0.130 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: 3 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: 302 Length of database: 305 Length adjustment: 27 Effective length of query: 275 Effective length of database: 278 Effective search space: 76450 Effective search space used: 76450 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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