GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Dyella japonica UNC79MFTsu3.2

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate N515DRAFT_3494 N515DRAFT_3494 sodium transport system ATP-binding protein

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3494
          Length = 244

 Score =  109 bits (273), Expect = 5e-29
 Identities = 80/240 (33%), Positives = 123/240 (51%), Gaps = 20/240 (8%)

Query: 5   ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64
           ++EV  L   FG + AV+GV     + Q+  ++GPNGAGKTT    L    +P  G I +
Sbjct: 1   MIEVKDLHKAFGAIKAVDGVGFSARDGQITGLLGPNGAGKTTTLRMLYTLMKPDRGQILV 60

Query: 65  DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENL-LVAQHRHLNTNFLAGLFKTPAF 123
           DG +    P     + GV+   +   L+K +TA EN+   A+   L  N LA        
Sbjct: 61  DGIDAAADPLAVRRQLGVLPDARG--LYKRLTARENIDYFARLHGLPENELA-------- 110

Query: 124 RRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAG 183
             S REA+      ++ + + E A+R     + GQ+ +  IAR ++  PR ++LDEP  G
Sbjct: 111 --SRREAL------VKALEMEEIADRRTEGFSQGQRVKTAIARALIHDPRNVILDEPTNG 162

Query: 184 LNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRD 243
           L+   T  L+  + KL++E    VL   H M+ V ++ D IVVI  G  +AD TP+ +R+
Sbjct: 163 LDVMATRALRQFMLKLKAEGR-CVLFSSHIMQEVAALCDRIVVIAHGRVVADETPQALRE 221


Lambda     K      H
   0.320    0.137    0.391 

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: 8
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: 255
Length of database: 244
Length adjustment: 24
Effective length of query: 231
Effective length of database: 220
Effective search space:    50820
Effective search space used:    50820
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.

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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