Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate 353166 BT3640 lipoprotein releasing system ATP-binding protein (NCBI ptt file)
Query= uniprot:A0A1N7U8S3 (276 letters) >FitnessBrowser__Btheta:353166 Length = 218 Score = 134 bits (338), Expect = 1e-36 Identities = 79/228 (34%), Positives = 135/228 (59%), Gaps = 14/228 (6%) Query: 27 LQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLD 86 +++EGI K +G +VLKG+ L +G+++S++G SG+GK+T+L+ + L++PDAG + +D Sbjct: 2 IKLEGITKSFGSLQVLKGIDLEINKGEIVSIVGPSGAGKTTLLQIMGTLDEPDAGTVAID 61 Query: 87 GISIEMRQGRAGTRAPHQDQLQNLRTR-LAMVFQHFNLWSHMTVLENITMAPRRVLDVSA 145 G + + + +L R + + VFQ L T LEN+ M P + VS+ Sbjct: 62 GTVVSRMK---------EKELSAFRNKNIGFVFQFHQLLPEFTALENV-MIPAFIAGVSS 111 Query: 146 AEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDP 205 EA +RA L +GL R A P LSGG++QRVA+ARAL P +IL DEP+ +LD Sbjct: 112 KEANERAMEILAFMGLTDR-ASHKPNELSGGEKQRVAVARALINHPAVILADEPSGSLDT 170 Query: 206 ELVGEVLKVIQTLAEE-GRTMLMVTHEMGFARQVSSQVLFLHQGRVEE 252 ++ ++ L + G+T ++VTH+ G A+ ++ + + + G +++ Sbjct: 171 HNKEDLHQLFFDLRDRLGQTFVIVTHDEGLAK-ITDRTVHMVDGTIKK 217 Lambda K H 0.319 0.133 0.372 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: 144 Number of extensions: 7 Number of successful extensions: 4 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: 276 Length of database: 218 Length adjustment: 24 Effective length of query: 252 Effective length of database: 194 Effective search space: 48888 Effective search space used: 48888 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 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