GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Dinoroseobacter shibae DFL-12

Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate 3607949 Dshi_1357 ABC transporter related (RefSeq)

Query= reanno::pseudo1_N1B4:Pf1N1B4_774
         (244 letters)



>FitnessBrowser__Dino:3607949
          Length = 349

 Score =  143 bits (360), Expect = 5e-39
 Identities = 78/217 (35%), Positives = 125/217 (57%), Gaps = 8/217 (3%)

Query: 2   ISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIVD 61
           I++  V KW+GD QV+     E++ GE +V  GPSG GKSTL++ +  LE   +G +++D
Sbjct: 4   ITLSKVEKWFGDVQVIKGVDLEIRDGEFVVFVGPSGCGKSTLLRMIGGLEDTSRGAMLID 63

Query: 62  GTSIADPKTNLPKLRSRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEASKKALQLL 121
           G  + D     P  +  + MVFQ + L+PH+S+ +N+  + +K  G    E ++K     
Sbjct: 64  GVDVTDH----PPAKRGLTMVFQSYALYPHMSVRENMGFS-LKTAGAPAAEIAEKVEAAA 118

Query: 122 ERVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMVQ 181
             + L  +  + P  LSGGQ+QRVAI R++   P   LFDEP S LD  +  E+   + +
Sbjct: 119 AVLKLEPYLDRRPKDLSGGQRQRVAIGRSIVRAPTAFLFDEPLSNLDAALRVEMRYEIAK 178

Query: 182 LAHEGM--TMMCVTHEMGFARKVADRVIFMDQGKIIE 216
           L H+ +  TM+ VTH+   A  +ADR++ ++ GKI +
Sbjct: 179 L-HQSLDTTMIYVTHDQVEAMTLADRIVVLEFGKIAQ 214


Lambda     K      H
   0.321    0.135    0.390 

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: 188
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: 244
Length of database: 349
Length adjustment: 26
Effective length of query: 218
Effective length of database: 323
Effective search space:    70414
Effective search space used:    70414
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: 48 (23.1 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