GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Lactobacillus silagei IWT126

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate WP_089136028.1 CES79_RS00805 amino acid ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc02121
         (258 letters)



>NCBI__GCF_002217945.1:WP_089136028.1
          Length = 246

 Score =  274 bits (701), Expect = 1e-78
 Identities = 139/241 (57%), Positives = 182/241 (75%), Gaps = 2/241 (0%)

Query: 19  IEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIVVD 78
           IE  N+ K+YGDFH L DINL +  GE +V+ GPSGSGKST+IR +N LE  Q+G+++V+
Sbjct: 4   IEFHNVQKYYGDFHALHDINLTIDAGETVVLIGPSGSGKSTLIRTVNGLERIQEGQLIVN 63

Query: 79  GIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKEAEQVAMHFL 138
           G +L N    ++ +R+ VGMVFQHFNL+ + TILEN  LAP  V K P++E +++AM  L
Sbjct: 64  GQDLANRKTDMNRIRKNVGMVFQHFNLYANKTILENIMLAPRLVLKRPEEENKKIAMDML 123

Query: 139 ERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVKEVLDTMVG 198
           +RV + +QA K P QLSGGQQQR+AIARSL MRPK LLFDEPTSALDPEM+ +VL+ M  
Sbjct: 124 DRVGLADQAPKMPAQLSGGQQQRIAIARSLAMRPKALLFDEPTSALDPEMIDDVLNVMKD 183

Query: 199 LA-EEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFD-NPQHERTKLFLSQI 256
           +A +  MTM+ VTHEMGFAR+VANRV+FM  G I+E +S  +FFD  P +ER + FLS+I
Sbjct: 184 IARDSSMTMLVVTHEMGFAREVANRVVFMADGHILEDDSKEKFFDGQPSNERARQFLSKI 243

Query: 257 L 257
           +
Sbjct: 244 I 244


Lambda     K      H
   0.322    0.136    0.397 

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: 219
Number of extensions: 4
Number of successful extensions: 3
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: 258
Length of database: 246
Length adjustment: 24
Effective length of query: 234
Effective length of database: 222
Effective search space:    51948
Effective search space used:    51948
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 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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