GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AGP1 in Paraburkholderia bryophila 376MFSha3.1

Align general amino acid permease AGP1 (characterized)
to candidate H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family

Query= CharProtDB::CH_091105
         (633 letters)



>FitnessBrowser__Burk376:H281DRAFT_04042
          Length = 506

 Score =  213 bits (543), Expect = 1e-59
 Identities = 139/433 (32%), Positives = 219/433 (50%), Gaps = 20/433 (4%)

Query: 112 KSDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCIIQA 171
           + D LK+ ++ RH+ +IALG  IGTGL +G+ + L  AGP+ +++GYAI G I + I++ 
Sbjct: 51  QQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPS-MILGYAIGGVIAFMIMRQ 109

Query: 172 CGEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYWTTS 231
            GEM +    + G ++ +      D  GF   W Y + ++ V   EL      + YW   
Sbjct: 110 LGEM-VAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPG 168

Query: 232 VNPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAGNDGF 291
           V   V  ++ +  +  IN+   + Y E EF+F   K++ + G  + G  + V G G    
Sbjct: 169 VPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGGPQA 228

Query: 292 IGGKYWHDPGAFNGKHAIDRFKGVAATLVTAAFAFGGSEFIAITTAEQSNPRKAIPGAAK 351
                W   G F   H    F G+   L    F+FGG E I IT AE   P+K+IP A  
Sbjct: 229 SISNLWSHGGFF--PHG---FHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVN 283

Query: 352 QMIYRILFLFLATIILLGFLVPYNSDQLLGSTGGGTKASPYVIAVASHGVRVVPHFINAV 411
           Q+IYRIL  ++ ++ +L  L P+N      + GG    SP+V+  +  G  +  + +N V
Sbjct: 284 QVIYRILIFYICSLAVLLSLYPWNEV----AAGG----SPFVMIFSQIGSTLTANVLNVV 335

Query: 412 ILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSAL--FAVIAFC 469
           +L + LS+ NS  Y+++R+   L+EQG AP+    +DR G P +A+G+SAL  F  +   
Sbjct: 336 VLTAALSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVN 395

Query: 470 AASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQTGVWGS 529
              P E       L ++ L  +  W  I L+HL+ RRAM   G +L    F      W  
Sbjct: 396 YLIPAEALGLLMALVVAAL--VLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNW-I 452

Query: 530 AYACIMMILILIA 542
             A + +IL+++A
Sbjct: 453 CLAFMALILVILA 465


Lambda     K      H
   0.324    0.138    0.424 

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: 756
Number of extensions: 31
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: 633
Length of database: 506
Length adjustment: 36
Effective length of query: 597
Effective length of database: 470
Effective search space:   280590
Effective search space used:   280590
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 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