Align glutamate-aspartate periplasmic-binding protein (characterized)
to candidate HSERO_RS17575 HSERO_RS17575 ABC transporter
Query= CharProtDB::CH_002441 (302 letters) >FitnessBrowser__HerbieS:HSERO_RS17575 Length = 305 Score = 309 bits (791), Expect = 6e-89 Identities = 152/302 (50%), Positives = 209/302 (69%), Gaps = 1/302 (0%) Query: 1 MQLRKPATAILALALSAGLAQADDAAPAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQ 60 + L PA A+L++ L+ QA A A G TL KI +I +GHR SS+PFSYYD Q Sbjct: 5 VNLAVPA-AMLSMMLAVLPQQACAADSALGPTLQKIKDANLIAIGHRTSSIPFSYYDENQ 63 Query: 61 KVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVER 120 +V+GYSQD N +++AVK K+ L+V+++P+TSQNR PLLQNGT D ECG T+N R Sbjct: 64 QVIGYSQDLCNKVIDAVKTKIGAAKLEVRMVPVTSQNRTPLLQNGTIDLECGVTSNLKSR 123 Query: 121 QKQAAFSDTIFVVGTRLLTKKGGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMNMR 180 +Q +F+ FV +R+LTK+ IKDF +L KAVV +GTTSE LL LNE +KM M+ Sbjct: 124 WQQVSFATNFFVASSRILTKRDSGIKDFPDLAGKAVVTNAGTTSEQLLRNLNEHRKMGMQ 183 Query: 181 IISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRK 240 I SAKD+G++F L+SGR A++MDD LLAG R A+KP++W + G P E Y M+R+ Sbjct: 184 IQSAKDYGEAFLILQSGRVAAYVMDDVLLAGARTTAQKPNDWVLTGNPFGAEPYAFMVRR 243 Query: 241 DDPQFKKLMDDTIAQVQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDKA 300 DDPQFK+L+DDT++ + SGE +K + KWF PIPPKN++ NF +SD + L+ P+DK Sbjct: 244 DDPQFKQLVDDTLSGLMKSGEIKKIYAKWFTFPIPPKNVSFNFPMSDTVMKLYATPSDKP 303 Query: 301 LN 302 ++ Sbjct: 304 MD 305 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: 260 Number of extensions: 12 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: 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