GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein

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



>FitnessBrowser__Dyella79:N515DRAFT_1562
          Length = 384

 Score =  157 bits (398), Expect = 2e-43
 Identities = 86/217 (39%), Positives = 138/217 (63%), Gaps = 8/217 (3%)

Query: 2   ISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIVD 61
           +SI+ + + YG F  L D S ++ +GE + + GPSGSGKS+L++ +  L+   +GDV+ D
Sbjct: 3   LSIRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLRD 62

Query: 62  GTSIADPKTNLPKLRSRVGMVFQHFELFPHLSIMDNLTIA-QVKVLGR--SKEEASKKAL 118
           GT +      LP  R  +G+VFQH+ LFPH+++ DN+    +V+   R  S+ + + +  
Sbjct: 63  GTDLLA----LPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVE 118

Query: 119 QLLERVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDV 178
            LL RV L    +++P QLSGGQ+QRVA+ARALA++P ++L DEP  ALD ++   +   
Sbjct: 119 DLLRRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVW 178

Query: 179 MVQLAHE-GMTMMCVTHEMGFARKVADRVIFMDQGKI 214
           +  L    G+T + VTH+   A ++ADRV+ M++G+I
Sbjct: 179 LRDLQRSLGLTTVLVTHDQDEALELADRVVVMNRGRI 215


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: 217
Number of extensions: 13
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: 384
Length adjustment: 27
Effective length of query: 217
Effective length of database: 357
Effective search space:    77469
Effective search space used:    77469
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