GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Pseudomonas putida KT2440

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate PP_2753 PP_2753 putative Branched-chain amino acid ABC transporter, ATP-binding protein

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__Putida:PP_2753
          Length = 257

 Score =  210 bits (534), Expect = 2e-59
 Identities = 114/232 (49%), Positives = 157/232 (67%), Gaps = 8/232 (3%)

Query: 10  YYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQA-----ASGSIRYEGEE 64
           Y G I A+  VS+ V +G+IV L+GANGAGKST L  + G  QA     + G IR++G++
Sbjct: 24  YDGTILAVAGVSLRVGQGDIVALLGANGAGKSTTLKAISGLVQADRAHVSRGHIRFQGQD 83

Query: 65  LVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMD--KVLELFPR 122
             G+ ++ + R+ I  V EGR VFS LT+EENL  GGF  +    Q++ D  ++   FPR
Sbjct: 84  TAGVAANLLARQGIVHVLEGRHVFSHLTIEENLRSGGFLRNPTRRQLEQDLERIYAWFPR 143

Query: 123 LKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLR-R 181
           LK + + +AG  SGGEQQMLAIGRALM+KP+L+LLDEPS+GLAPII+++IF I+ QL  +
Sbjct: 144 LKTKRKTQAGLTSGGEQQMLAIGRALMTKPRLVLLDEPSMGLAPIIVEEIFAIVAQLNAQ 203

Query: 182 EGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLGG 233
           +GV+  + EQN N AL+ A  AY+LENGR+V   + A L     ++  YLGG
Sbjct: 204 QGVSFLVAEQNINVALRYASHAYILENGRVVGEGSAAELAAREDIQHFYLGG 255


Lambda     K      H
   0.318    0.136    0.374 

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: 161
Number of extensions: 5
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: 233
Length of database: 257
Length adjustment: 24
Effective length of query: 209
Effective length of database: 233
Effective search space:    48697
Effective search space used:    48697
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 (21.7 bits)
S2: 46 (22.3 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