GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Novosphingobium fuchskuhlense FNE08-7

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_082697561.1 AQZ52_RS05130 amino acid permease

Query= TCDB::Q2VQZ4
         (536 letters)



>NCBI__GCF_001519075.1:WP_082697561.1
          Length = 469

 Score =  159 bits (403), Expect = 2e-43
 Identities = 127/424 (29%), Positives = 199/424 (46%), Gaps = 31/424 (7%)

Query: 24  ETGEVKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLL 83
           E G   +  L + L  RH+ MIAIGG IGAGLFVGS   +   GPAA +I YLI G+++L
Sbjct: 17  EAGGAGSVELSRTLLPRHVSMIAIGGIIGAGLFVGSSTTIALTGPAA-VISYLIAGLLIL 75

Query: 84  CTCLALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRF 143
                +AEMA++      F  +    +    GF  GW Y   W+ V+  E IA +  I  
Sbjct: 76  LVMRMIAEMAIVLEGVRTFPDFARAGLGHLAGFLSGWLYWYFWVVVVAVEAIAGAKIIGG 135

Query: 144 WREDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVG 203
           W   +      +    ++ G+ +   R YGE EF  S IK+ A + F ++  +   G   
Sbjct: 136 WLPGVPEWAIGAGLTALMTGVNLMSTRSYGEFEFWFSSIKVAAILVFSLICALWVFGITA 195

Query: 204 DQGYIGVKYWRDPGAFTSFKGFC--------AVFVVAAFSFGGTEMVGLAAAESANPRKS 255
            QG+         G  T+  GF         A      FS  G E+  +AAAES +P K 
Sbjct: 196 PQGF-------SIGNLTAHGGFAPHGWGPVLAGVASTIFSLCGAEIATIAAAESPDPAKV 248

Query: 256 IPMASKQVFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLP 315
           I   +  V  RI IFY+L + ++  ++P                SPF   +    I    
Sbjct: 249 IARMTVSVALRIVIFYVLAIGLIVAVVPWTQ--------IVPGHSPFATTLAAMHIPGGE 300

Query: 316 SIMNAVITVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGL 375
           +IM+AV+ VAVLS  NS  + ++R +  +A    AP++  +++++G P   +   IA  L
Sbjct: 301 TIMSAVVLVAVLSCLNSGLYVTSRALFGLARFGDAPDWLVHVNARGVPARAI---IAASL 357

Query: 376 LAYIGAAPQGME---IFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQG-INLGLIPYK 431
            AY   A Q +    +F +L+  +G+  + ++  + +A ++ R  M+ +    L L  + 
Sbjct: 358 FAYGALAAQWLSPGTVFSFLVNSSGVTMILLYALVGIAQLKERTRMEREAPERLTLKMWF 417

Query: 432 TPFG 435
            PFG
Sbjct: 418 HPFG 421


Lambda     K      H
   0.327    0.142    0.442 

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: 595
Number of extensions: 24
Number of successful extensions: 6
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: 536
Length of database: 469
Length adjustment: 34
Effective length of query: 502
Effective length of database: 435
Effective search space:   218370
Effective search space used:   218370
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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