GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prdC in Bacteroides thetaiotaomicron VPI-5482

Align Electron transfer protein (characterized, see rationale)
to candidate 350146 BT0618 Na+-transporting NADH:ubiquinone oxidoreductase, Electron transport complex protein rnfC (NCBI ptt file)

Query= uniprot:E3PU00
         (428 letters)



>lcl|FitnessBrowser__Btheta:350146 BT0618 Na+-transporting
           NADH:ubiquinone oxidoreductase, Electron transport
           complex protein rnfC (NCBI ptt file)
          Length = 445

 Score =  146 bits (369), Expect = 1e-39
 Identities = 102/325 (31%), Positives = 162/325 (49%), Gaps = 25/325 (7%)

Query: 4   VLLLKQHVGAPCQSIVEAGQKVQKGELIAKPNG-LGANLHSSVYGVVKAVN--------- 53
           V+LL QH+GAP + IV  G  V+ G  IA+P G + A +HSSV G V  ++         
Sbjct: 33  VILLGQHIGAPAKPIVAKGDMVKVGTKIAEPAGFVSAAIHSSVSGKVAKIDTVVDASGYA 92

Query: 54  ETAIIIEADENQPDEFVKIKDTNTH---------IEAIQEAGIVGSGGAGFPTHVKL--N 102
           + AI I+ + ++ +E +    T            ++ I +AGIVG GGA FPT VKL   
Sbjct: 93  KPAIFIDVEGDEWEETIDRSKTLVKECELSSEEIVKKIADAGIVGLGGACFPTQVKLCPP 152

Query: 103 VNLEGGYVIANGAECEPVLGHNIKLMEEDPQLIIRGLKYVKEITNASKAYIAMKAKHRKA 162
            + +   VI N  ECEP L  + +LM E  + ++ G+  + +    +KA+I ++     A
Sbjct: 153 PSFKAECVIINAVECEPYLTADHQLMLEHAEEVMVGVSILMKAVKVNKAFIGIENNKPDA 212

Query: 163 LRILKTACELEPDIEVKILPDMYPAGDERAIVRDILGVLLEPGQLPKAANAVIQNVETLK 222
           + ++         IEV  L   YP G E+ ++  I    +  G LP +  AV+QNV T  
Sbjct: 213 IELMTKVASSYAGIEVVPLKVKYPQGGEKQLIDAITKRQVASGALPISTGAVVQNVGTAF 272

Query: 223 HIVNAIELRKPYITKDITVAGRVMDATDGKVFMDVPVGESVKKYIDLCGGYMNPHGEIVM 282
            +  A++  KP   + ITV G+ +      +     +G  +K+ ID CGG     G+++ 
Sbjct: 273 AVYEAVQKNKPLFERVITVTGKSVAKPSNFL---ARIGTPMKQLIDACGGLPEDTGKVIG 329

Query: 283 GGPFTGRHVEE-DAPITKTTGGILV 306
           GGP  G+ +   + P  K + GIL+
Sbjct: 330 GGPMMGKALMNIEVPTAKGSSGILI 354


Lambda     K      H
   0.318    0.137    0.399 

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: 500
Number of extensions: 28
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: 428
Length of database: 445
Length adjustment: 32
Effective length of query: 396
Effective length of database: 413
Effective search space:   163548
Effective search space used:   163548
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: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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