Align glutamate-aspartate periplasmic-binding protein (characterized)
to candidate H281DRAFT_02625 H281DRAFT_02625 amino acid ABC transporter substrate-binding protein, PAAT family
Query= CharProtDB::CH_002441 (302 letters) >FitnessBrowser__Burk376:H281DRAFT_02625 Length = 301 Score = 341 bits (874), Expect = 1e-98 Identities = 170/294 (57%), Positives = 207/294 (70%), Gaps = 4/294 (1%) Query: 7 ATAILALALSAGLAQADDAAPAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYS 66 A A+ L+L G + + P TL KI +I VGHRE+SVPFSY D VVG+S Sbjct: 10 AFALATLSLVTGTSYGQGSQP----TLAKIESTNLIAVGHRETSVPFSYVDTNNNVVGFS 65 Query: 67 QDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAF 126 QD N +++AVK K PDL+V+ IP+TSQNRIPL+QNGT D ECG TTN RQ Q AF Sbjct: 66 QDLCNKVIDAVKLKTKHPDLRVRFIPVTSQNRIPLVQNGTIDLECGVTTNLTARQNQVAF 125 Query: 127 SDTIFVVGTRLLTKKGGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKD 186 SDT FV TRLLT+K IKDF +L K VV GTTSE +L K+NEE+KMNM IISAKD Sbjct: 126 SDTFFVATTRLLTRKDSGIKDFPDLAGKTVVTNQGTTSERILRKMNEEKKMNMSIISAKD 185 Query: 187 HGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDPQFK 246 +G+ TLE+GRAVA+MMDD LLAG R+ KP +W +VG PQS EAYG M+RKDDP+FK Sbjct: 186 YGEGRATLETGRAVAYMMDDVLLAGTRSLTAKPSDWALVGTPQSSEAYGFMMRKDDPEFK 245 Query: 247 KLMDDTIAQVQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDKA 300 KL+DD ++QV S E + +DKWF P+PPKN+N F +S M+ LF EPNDKA Sbjct: 246 KLVDDAMSQVMRSPEIKTLYDKWFTKPVPPKNINFEFPMSGTMQKLFAEPNDKA 299 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: 290 Number of extensions: 8 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: 301 Length adjustment: 27 Effective length of query: 275 Effective length of database: 274 Effective search space: 75350 Effective search space used: 75350 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