GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Bacteroides thetaiotaomicron VPI-5482

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 353284 BT3758 acetylornithine aminotransferase (NCBI ptt file)

Query= BRENDA::Q9I6M4
         (426 letters)



>FitnessBrowser__Btheta:353284
          Length = 373

 Score =  199 bits (506), Expect = 1e-55
 Identities = 134/392 (34%), Positives = 207/392 (52%), Gaps = 45/392 (11%)

Query: 30  RAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIE 89
           + +   VWD  G EY+D  GG AV++ GH HP  +  +  Q+  L      V+      +
Sbjct: 16  KGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATLGFYSNSVIN-----K 70

Query: 90  LAEEIAKR---VPGDFPKKTLLVTSGSEAVENAVKIARAATGRAGVIAFTGAYHGRTMMT 146
           L +++A+R   + G       L+ SG+EA ENA+K+A    GR  VI+F+ A+HGRT + 
Sbjct: 71  LQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFSKAFHGRTSLA 130

Query: 147 LGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQDIAAIII 206
           +  T                    +AP   +G      +  IE + K +    D+ A+II
Sbjct: 131 VEATNNPT---------------IIAPINNNGHVTYLPLNDIEAM-KQELAKGDVCAVII 174

Query: 207 EPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPDLTT 266
           E +QG GG  + +  FMQ LR +C + G +LI DE+Q+G GR+G FFA +   I PD+ T
Sbjct: 175 EGIQGVGGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIIT 234

Query: 267 FAKSVGGGFPISGVAGKAEIMDAIAP--GGLGGTYAGSPIACAAALAVLKVFEEEKLLER 324
            AK +G GFP++GV     I     P  G LG T+ G+ +AC+AALAV+ V E++ L+E 
Sbjct: 235 VAKGIGNGFPMAGVL----ISPMFKPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVEN 290

Query: 325 SQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRAREK 384
           ++AVG+ L   L+    K   I +VRG G M+ +E  E      P  EL S+++    ++
Sbjct: 291 AKAVGDYLLEELK----KFPQIKEVRGRGLMIGLEFEE------PIKELRSRLIY---DE 337

Query: 385 GLILLSCGTYYNVIRFLMPVTIPDAQLEKGLA 416
            +   + GT  NV+R L P+ +   + ++ LA
Sbjct: 338 HVFTGASGT--NVLRLLPPLCLSMEEADEFLA 367


Lambda     K      H
   0.319    0.137    0.393 

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: 345
Number of extensions: 18
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: 426
Length of database: 373
Length adjustment: 31
Effective length of query: 395
Effective length of database: 342
Effective search space:   135090
Effective search space used:   135090
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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