GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Chryseobacterium arthrosphaerae CC-VM-7

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_065399245.1 BBI00_RS13465 amino acid permease

Query= TCDB::Q2VQZ4
         (536 letters)



>NCBI__GCF_001684965.1:WP_065399245.1
          Length = 473

 Score =  220 bits (561), Expect = 8e-62
 Identities = 136/426 (31%), Positives = 213/426 (50%), Gaps = 33/426 (7%)

Query: 20  TRDVETGEVKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIG 79
           + +  TGE  N  L + L NRH+Q+IA+GGAIG GLF+G G A    GP+ +L GY + G
Sbjct: 2   SNEKNTGE--NETLVRGLTNRHIQLIALGGAIGTGLFLGIGPAAVLAGPSVIL-GYALAG 58

Query: 80  IMLLCTCLALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASI 139
           I+       L EM V  PV+G+F  +  ++     GFA GW Y + ++ V   EL A   
Sbjct: 59  IIAFFIMRQLGEMVVQEPVSGSFSHFAYKYWGNFPGFASGWNYWILYILVSMAELTAIGH 118

Query: 140 TIRFWREDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINC 199
            I FW  +I + V    F VV+  + +  V+ YGE EF  SIIK+ A +  I+ G+ +  
Sbjct: 119 YIHFWWPEIPLWVSSLFFFVVITALNLASVKVYGETEFWFSIIKVIAIIAMIVFGVYLLV 178

Query: 200 GGVGDQGYIGVKYWRDPGAF---------TSFKGFCAVFVVAAFSFGGTEMVGLAAAESA 250
            G G +       W D G F           F G  A   +  FSFGG E++G+ AAE+ 
Sbjct: 179 SGTGGEKATITNLWNDGGFFPKGLFNKTENGFSGLFAAMAMIMFSFGGLELIGITAAEAK 238

Query: 251 NPRKSIPMASKQVFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDA- 309
           NP K+IP A+ QV +RI IFY+  L I+  + P  +            +SPFV+  Q+  
Sbjct: 239 NPEKTIPQATNQVIYRILIFYVGALVILFSLSPWRE--------ITEGSSPFVMVFQNLN 290

Query: 310 GIK------------VLPSIMNAVITVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYI 357
           G++            ++ +++N ++  A LSV NS  + ++R +  +A++  AP F K +
Sbjct: 291 GLEFSLFGKVIQFNSLIANVLNLIVLTAALSVYNSSVYSNSRMLFGLAQQGNAPKFLKKL 350

Query: 358 DSKGRPLYCVILQIAFGLLAYIGAAPQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAG 417
           +    P   +++   F  +  I       + F +L+AL     +  W  IC  H++ +  
Sbjct: 351 NKNSVPTNAILISSCFAGICIIINKLVPEKAFQYLMALVVSTLIINWLMICYTHLKFKKA 410

Query: 418 MKAQGI 423
           +  +GI
Sbjct: 411 ITREGI 416


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: 620
Number of extensions: 35
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: 536
Length of database: 473
Length adjustment: 34
Effective length of query: 502
Effective length of database: 439
Effective search space:   220378
Effective search space used:   220378
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