Align ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component (characterized)
to candidate HSERO_RS19255 HSERO_RS19255 ABC transporter
Query= reanno::pseudo1_N1B4:Pf1N1B4_771 (304 letters) >FitnessBrowser__HerbieS:HSERO_RS19255 Length = 315 Score = 290 bits (741), Expect = 4e-83 Identities = 149/290 (51%), Positives = 197/290 (67%), Gaps = 1/290 (0%) Query: 7 ILGAAIAAALISTPVFAAELTGTLKKIKESGTITLGHRDASIPFSYIADASGKPVGYSHD 66 + G + A+++ + V A E TG LKKIK+SGT+TLG RD+SIPFSY+ D GYS D Sbjct: 6 LAGVLVGASVLMSSVHAEEFTGRLKKIKDSGTLTLGVRDSSIPFSYLDDKQSYQ-GYSID 64 Query: 67 IQLKIVEAIKKDLDMPNLQVKYNLVTSQTRIPLVQNGTVDVECGSTTNNVERQQQVDFSV 126 + LK AI+K L + +L +K VTS TRIPL+ NGT D+ C S TNN ER QV FSV Sbjct: 65 LCLKAATAIQKKLGLTSLNIKMVPVTSATRIPLIANGTTDISCDSATNNQERWNQVAFSV 124 Query: 127 GIFEIGTKLLSKKDSAYKDFADLKGKNVVTTAGTTSERILKSMNADKQMGMNVISAKDHG 186 F K LSKK + K DLKGK VV+T+GT++ + + ++NA++ +GMN+++AKDH Sbjct: 125 TEFVTANKFLSKKAANLKTLEDLKGKTVVSTSGTSNLKQITALNAERNLGMNILAAKDHA 184 Query: 187 ESFQMLETGRAVAFMMDDALLAGEMAKAKKPTDWAVTGTAQSNEIYGCMVRKGDAPFKKA 246 E+F M+ETGRA AF+MDD LL+ A +K P D+ V+ A S E YG ++ KGD FK Sbjct: 185 EAFLMVETGRAAAFVMDDILLSSLAANSKAPGDYQVSSEALSVEPYGLILPKGDKEFKTV 244 Query: 247 VDDAIIATYKSGEINKIYEKWFMQPIPPKGLNLMFPMSEELKALIANPTD 296 VDDA+ YK +I KIY KWF PIPPKG+NL PMS +L+A++A PTD Sbjct: 245 VDDALTVVYKGDDIKKIYAKWFQSPIPPKGVNLNVPMSPQLQAVLAKPTD 294 Lambda K H 0.315 0.131 0.365 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: 245 Number of extensions: 8 Number of successful extensions: 2 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: 304 Length of database: 315 Length adjustment: 27 Effective length of query: 277 Effective length of database: 288 Effective search space: 79776 Effective search space used: 79776 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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