Align glutamate-aspartate periplasmic-binding protein (characterized)
to candidate BPHYT_RS29570 BPHYT_RS29570 ABC transporter
Query= CharProtDB::CH_002441 (302 letters) >FitnessBrowser__BFirm:BPHYT_RS29570 Length = 291 Score = 329 bits (843), Expect = 5e-95 Identities = 164/292 (56%), Positives = 205/292 (70%), Gaps = 1/292 (0%) Query: 11 LALALSAGLAQADDAAPAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYS 70 +ALA A + +A STL KI I +GHRE+SVPFSY D +V+G+SQD Sbjct: 1 MALATFA-VVSTSASAQETQSTLAKIRSGNSISIGHRETSVPFSYVDTNNQVIGFSQDIC 59 Query: 71 NAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSDTI 130 N I++AVK K PDL V+ IP+TSQNRIPL+QNGT D ECG TTN RQ Q AFSDT Sbjct: 60 NRIIDAVKAKTGHPDLHVRFIPVTSQNRIPLVQNGTVDLECGVTTNLTSRQNQVAFSDTF 119 Query: 131 FVVGTRLLTKKGGDIKDFANLKDKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDS 190 FV TRLLT+K IKDF +L K VV GTTSE LL K+NEE+KMNM+IISAKD+G+ Sbjct: 120 FVATTRLLTRKDSGIKDFTDLAGKTVVTNQGTTSERLLRKMNEEKKMNMQIISAKDYGEG 179 Query: 191 FRTLESGRAVAFMMDDALLAGERAKAKKPDNWEIVGKPQSQEAYGCMLRKDDPQFKKLMD 250 TLE+GRAVA+MMDD LLAG R+ KP +W IVG PQS EAYG MLRKDDP+FK+L+D Sbjct: 180 RVTLETGRAVAYMMDDVLLAGARSLTAKPADWVIVGAPQSSEAYGFMLRKDDPEFKRLVD 239 Query: 251 DTIAQVQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDKALN 302 D + +V E + +DKWF P+PPK +N +F +S+ ++ L+ PND+A + Sbjct: 240 DAMVRVMKGSEIKTLYDKWFLKPVPPKGINFDFPMSEALEKLYATPNDRAFD 291 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: 266 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: 291 Length adjustment: 26 Effective length of query: 276 Effective length of database: 265 Effective search space: 73140 Effective search space used: 73140 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