Align glutamate-aspartate periplasmic-binding protein (characterized)
to candidate H281DRAFT_04270 H281DRAFT_04270 L-glutamate-binding protein /L-aspartate-binding protein
Query= CharProtDB::CH_002441 (302 letters) >FitnessBrowser__Burk376:H281DRAFT_04270 Length = 297 Score = 391 bits (1004), Expect = e-113 Identities = 192/302 (63%), Positives = 243/302 (80%), Gaps = 5/302 (1%) Query: 1 MQLRKPATAILALALSAGLAQADDAAPAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQ 60 M+++K A + L L A A DA TL KI GVI +GHRESS+PFSYYD++Q Sbjct: 1 MKVKKAALLLATLGLFTVGAHAQDAG-----TLKKIKDTGVISLGHRESSIPFSYYDDKQ 55 Query: 61 KVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVER 120 V+GYSQ+++ +V+AVK+KLN P+L+VKL P+TSQNRIPL+QNGT D ECGSTTNN ER Sbjct: 56 NVIGYSQEFALKVVDAVKQKLNMPNLKVKLTPVTSQNRIPLVQNGTVDMECGSTTNNAER 115 Query: 121 QKQAAFSDTIFVVGTRLLTKKGGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMNMR 180 Q+Q AFS+TIFV+GTRL+TKK IKD+A+LK K VV T+GTTSE LL K+N+++ M M Sbjct: 116 QQQVAFSNTIFVIGTRLMTKKDSGIKDWADLKGKTVVTTAGTTSERLLRKMNQDKSMGMN 175 Query: 181 IISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRK 240 IISAKDHG+SF TL +GRA AFMMDDALLAGERAK+ P+++ IVG PQS EAYGCMLRK Sbjct: 176 IISAKDHGESFLTLSTGRAAAFMMDDALLAGERAKSNTPNDFVIVGAPQSHEAYGCMLRK 235 Query: 241 DDPQFKKLMDDTIAQVQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDKA 300 +DP+FKK++DD IA+V+TSGEA++ + KWF+ PIPPK LN+NF SD++KALFK PNDKA Sbjct: 236 NDPEFKKVVDDAIAKVETSGEADQIYKKWFETPIPPKGLNLNFPESDDIKALFKSPNDKA 295 Query: 301 LN 302 ++ Sbjct: 296 ID 297 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: 319 Number of extensions: 7 Number of successful extensions: 1 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: 297 Length adjustment: 27 Effective length of query: 275 Effective length of database: 270 Effective search space: 74250 Effective search space used: 74250 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